User Manual for MALT V0.1.2 - Algorithms in Bioinformatics
Contents
1. d index g2t MALT data gi_taxid_prot 2014Jan04 bin tre MALT data ncbi tre gz map MALT data ncbi tre gz L megan5 license txt The input files are specified using i the index is specified using d The option g2t is used to specify a GI to taxon id mapping which will be used to identify the taxa associated with the reference sequences A mapping file is supplied in the data directory of MALT The options tre and map are used to access the NCBI taxonomy which is needed to perform a taxonomic analysis of the reads as they are aligned Use L to explicitly provide a MEGANS license file to the program if you have not previously used a licensed version of MEGAN5S Then use malt run to analyze a file of DNA reads Assume that the DNA reads are contained in two files reads1 fna and reads2 fna Call the program as follows malt run i readsi fna reads2 fna d index m BlastX o L megand license txt If either of the two programs abort due to lack insufficient memory then please end the files malt bin malt build and or malt bin malt run By default for testing purposes the memory reserved for the programs is set to 10GB For comparison against the NCBI NR database for example you will need about 300GB All input files are specified using i Because loading of the index may take a long time it is best to launch the program on a large number of files The index to use is specified using d The option m defines the alignment mode of t2. lowing four shapes 111101101110111 1111000101011001111 11101001001000100101111 and 11101001000010100010100111 These seeds were suggested in 5 see http www biomedcentral com content supplementary 1471 2164 12 280 s1 pdf maxHitsPerSeed Use to specify the maximum number of hits per seed The program uses this to calculate a maximum number of hits per hash value proteinReduct Use this to specify the alphabet reduction in the case of protein reference sequences By default the program reduces amino acids to 8 different letters grouped as follows LVIMC AG ST P FYW EDNQ KR H This is referred to as the BLOSUM50_8 reduction in MALT and was suggested in 8 There are numerous options that can be used to provide mapping files to malt build for classifi cation support These are used by the program to map reference sequences or genes to taxonomic and or functional classes g2t r2t s2t Use to specify mapping files to map reference sequences to taxonomic identifiers NCBI taxon integer ids Use g2t for a file mapping GI numbers to taxon ids Use r2t for a file mapping RefSeq identifiers to taxon ids Use s2t for a file that maps synonyms to taxon ids A synonym is any word that may occur in the header line of a reference sequence g2k r2k s2k Use to specify mapping files to map reference sequences to KEGG KO numbers 6 The detailed usage of three different options is analogous to above g2s r2s s2s Use t
3. v verbose Echo commandline options and be verbose Default value false h help Show program usage and quit Figure 2 Summary of command line usage of malt run 13 BLOSUM90 References 1 Stefan Burkhardt and Juha K rkk inen Better filtering with gapped q grams Fundamenta Informat icae XXIII 1001 1018 2001 2 Kun Mao Chao William R Pearson and Webb Miller Aligning two sequences within a specified diagonal band Computer Applications in the Biosciences 8 5 481 487 1992 3 D H Huson A F Auch J Qi and S C Schuster MEGAN analysis of metagenomic data Genome Res 17 3 377 386 March 2007 4 Daniel H Huson Suparna Mitra Nico Weber Hans Joachim Ruscheweyh and Stephan C Schuster Integrative analysis of environmental sequences using MEGAN4 Genome Research 21 1552 1560 2011 5 Lucian Ilie Silvana Ilie Shima Khoshraftar and Anahita Mansouri Bigvand Seeds for effective oligonu cleotide design BMC Genomics 12 280 2011 6 M Kanehisa and S Goto KEGG Kyoto encyclopedia of genes and genomes Nucleic Acids Res 28 1 27 30 Jan 2000 7 Bin Ma John Tromp and Ming Li PatternHunter faster and more sensitive homology search Bioin formatics 18 3 440 445 2002 8 Lynne Reed Murphy Anders Wallqvist and Ronald M Levy Simplified amino acid alphabets for protein fold recognition and implications for folding Protein Engineering 13 149 152 4 2000 9 Z Ning A J Cox
4. This type of license is granted for a charge from the University of Tiibingen please contact Daniel Huson for details e Site license This license permits use of the program at a single physical location within a single organization This type of license is granted for a charge from the University of T bingen please contact Daniel Huson for details e Enterprise license This license permits use of the program anywhere within a single organi zation This type of license is granted for a charge from the University of Tiibingen please contact Daniel Huson for details e Evaluation license This type of license is granted for 45 days and is for evaluation purposes only It is available free of charge from the University of Tubingen please contact Daniel Huson for details 5 The MALT index builder The first step in a MALT analysis is to build an index for the given reference database This is done using a program called malt build In summary malt build takes a reference sequence database represented by one or more FastA files possibly in gzip format as input and produces an index that then can subsequently be used by the main analysis program malt run as input If MALT is to be used as an taxonomic and or functional analysis tool as well as an alignment tool then in addition malt build must be provided with a number of mapping files that are used to map reference sequences to taxonomic or functional classes or to locate genes in DNA
5. and J C Mullikin SSAHA a fast search method for large DNA databases Genome Res 11 10 1725 1729 2001 10 Ross Overbeek Tadhg Begley Ralph M Butler Jomuna V Choudhuri Han Yu Chuang Matthew Cohoon Val rie de Cr cy Lagard Naryttza Diaz Terry Disz Robert Edwards Michael Fonstein Ed D Frank Svetlana Gerdes Elizabeth M Glass Alexander Goesmann Andrew Hanson Dirk Iwata Reuyl Roy Jensen Neema Jamshidi Lutz Krause Michael Kubal Niels Larsen Burkhard Linke Alice C McHardy Folker Meyer Heiko Neuweger Gary Olsen Robert Olson Andrei Osterman Vasiliy Portnoy Gordon D Pusch Dmitry A Rodionov Christian Riickert Jason Steiner Rick Stevens Ines Thiele Olga Vassieva Yuzhen Ye Olga Zagnitko and Veronika Vonstein The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res 33 17 5691 5702 2005 11 Sean Powell Damian Szklarczyk Kalliopi Trachana Alexander Roth Michael Kuhn Jean Muller Roland Arnold Thomas Rattei Ivica Letunic Tobias Doerks Lars Juhl Jensen Christian von Mering and Peer Bork eggNOG v3 0 orthologous groups covering 1133 organisms at 41 different taxonomic ranges Nucleic Acids Research 40 Database Issue 284 289 2012 12 R L Tatusov E V Koonin and D J Lipman A genomic perspective on protein families Science 278 5338 631 637 Oct 1997 13 Yongan Zhao Haixu Tang and Yuzhen Ye RAPSearch 2 a fast and mem
6. 25 Maximum number of non overlapping alignments per reference Default value 1 Match score Default value 2 Mismatch score Default value 3 Parameter Lambda for BLASTN statistics Default value 0 625 Parameter K for BLASTN statistics Default value 0 41 Protein substitution matrix to use Default value BLOSUM62 Legal values BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 Align query forward strand only Default value false Align query reverse strand only Default value false Top percent value for LCA algorithm Default value 10 0 Min support value for LCA algorithm as a percent of assigned reads 0 off Default value 0 001 Min support value for LCA algorithm overrides minSupportPercent Default value 1 Maximum number of seed matches per offset per read frame Default value 100 Maximum number of seed matches per read and reference Default value 20 Seed shift Default value 1 Gap open penalty Default value 11 Gap extension penalty Default value 1 Band width 2 for banded alignment Default value 4 Properties file Default value Users huson Library Preferences Megan def L licenseFile string Specify license file Default value Users huson etc megan5 license txt Other rqcb replicateQueryCacheBits number Bits used for caching replicate queries size is then 2 bits Default value 20 xP xPart Show part of the table in human readable form for debugging Default value false
7. File specification possibilities as for alignments gzipAligned Compress aligned reads output using gzip Default value true outUnaligned Use this to specify that all reads that do not have any significant alignment to any reference sequence should be saved File specification possibilities as for alignments gzipUnaligned Compress unaligned reads output using gzip Default value true There are three performance related options threads Use to set the number of threads to use in parallel computations Default is 8 Set this to the number of available cores rqc Cache results for replicated queries maxTables Use to set the maximum number of seed tables to use 0 all Default value 0 replicateQueryCache Use to turn on caching of replicated queries This is especially useful for processing 16S datasets in which identical sequences occur multiple times Turning on this feature does not change the output of the program but can cause a significant speed up Default value false 10 The most important performance related option is the maximum amount of memory that malt run is allowed to use This cannot be set from within the program but rather is set during installation of the software The following options are used to filter matches by significance Matches that do not meet all criteria specified are completely ignored minBitScore Minimum bit score Default value 50 0 maxExpected Maximum expected score De
8. Waterman or semi global alignments in which reads are aligned end to end into reference sequences the latter being more appropriate for aligning metagenomic reads to references By default MALT produces a MEGAN RMA file that contains taxonomic and functional classi fications of the reads that can be opened in MEGAN The taxonomic analysis use the naive LCA algorithm introduced in 4 Used as an alignment tool MALT can produce alignments in BLAST text format BLAST tab format or SAM format both for DNA and protein alignments In addition the program can be used as a filter to obtain all reads that have a significant alignment or do not have a significant alignment to the given reference database MALT can also be used to compute a taxonomic analysis of 16S sequences Here the ability to compute a semi global alignment rather than a local alignment is crucial When provided with a listing of gene locations and annotations for a given database of DNA sequences MALT is able to predict genes based on BLASTN style alignments MALT actually consists of two programs malt build and malt run The malt build program is first used to build an index for the given reference database It can index arbitrary large databases provided the used computer has enough memory For maximum speed the program uses a hash table and thus require a large memory machine The malt run program is then used to perform alignments and analyses MALT does
9. align one or more files of input sequences DNA or proteins against an index representing a collection of reference DNA or protein sequences In a preprocessing step the index is computed using the malt build as described above Depending on the type of input and reference sequences the program can be be run in BLASTN BLASTP or BLASTX mode The malt run program is controlled by command line options see Figure 2 The first options specifies the program mode and alignment type mode Use this to run the program in BlastN mode BlastP mode or BlastX mode that is to align DNA and DNA protein and protein or DNA reads against protein references respectively Obviously the former mode can only be used if the employed index contains DNA sequences whereas the latter two modes are only applicable to an index based on protein reference sequences alignmentType Use this to specify the type of alignments to be performed By default this is set to Local and the program performslocal alignment just like BLAST programs do Alternatively this can be set to SemiGlobal in which case the program will perform semi global alignment in which reads are aligned end to end There are two options for specifying the input inFile Use this to specify all input files Input files must be in FastA or FastQ format and may be gzipped in which case their names must end on gz index Use this to specify the directory that contains the index built by
10. not use a new approach but is rather a new carefully crafted implementation of existing approaches The program uses spaced seeds rather than consecutive seeds 1 7 It uses a hash table to store seed matches see for example 9 It uses a reduced alphabet to determine potential matches between protein sequences 8 13 Finally it uses a banded alignment algorithm 2 that can compute both local and semi global alignments Both programs make heavy use of parallelization and require a lot of memory The ideal hardware requirements are a linux server with 64 cores and 512 GB of memory MALT performs alignment and analysis of high throughput sequencing data in a high throughput manner Here are some examples 1 Using the RefSeq microbial protein database version 50 containing 10 million protein se quences with a total length of 3 2 billion amino acids a BLAST X style analysis of taxonomic and functional content of a collection of 11 million Illumina reads takes about 900 wall clock seconds using 64 cores The program found about 4 5 million significant alignments covering about 15 of the total reads 2 Using the Genbank DNA database microbes and viruses downloaded early 2013 containing about 2 3 million DNA sequences with a total length of 11 billion nucleotides a BLASTN style analysis of one million reads takes about 70 wall clock seconds The program finds about two million significant alignments covering one quarter of the tot
11. User Manual for MALT V0 1 2 Daniel H Huson June 4 2015 Contents Contents 1 1 Introduction 1 2 Getting Started 4 3 Obtaining and Installing the Program 5 4 Licensing 5 5 The MALT index builder 6 6 The MALT analyzer 9 References 14 Index 15 1 Introduction Disclaimer This software is provided AS IS without warranty of any kind This is develop mental code and we make no pretension as to it being bug free and totally reliable Use at your own risk We will accept no liability for any damages incurred through the use of this software Use of MALT is free for academic usage however the program is not open source MALT an acronym for MEGAN alignment tool or MEGAN alignment tool is a sequence alignment and analysis tool designed for processing high throughput sequencing data especially in the context of metagenomics It is an extension of MEGAN the MEGenome Analyzer and is designed to provide the input for MEGAN but can also be used independently of MEGAN The core of the program is an sequence alignment engine that aligns DNA or protein sequences to a DNA or protein reference database in either BLASTN DNA queries and DNA references BLASTX DNA queries and protein references or BLASTP protein queries and protein refer ences mode The engine uses a banded alignment algorithm with affine gap scores and BLOSUM substitution matrices in the case of protein alignments The program can compute both local alignments Smith
12. al reads 3 Using the Silva database SSURef NR99_115 tax_silva fasta containing 479 726 DNA se quences with a total length of 690 million nucleotides the semi global alignment of 5000 16S reads takes about 100 seconds using 64 cores producing about 100 000 significant alignments This document provides both an introduction and a reference manual for MALT 2 Getting Started This section describes how to get started Download the program from http www ab informatik uni tuebingen de software malt see Section 3 for details Then make sure that you have a license certificate for MEGAN5 This license is required to run MALT First use malt build to build an index for MALT For example to build an index for all viral pro teins in RefSeq download the following file ftp ftp ncbi nlm nih gov refseq release viral viral 1 protein faa gz Put this file in a single directory called references say There is no need to unzip the file because MALT is able to read zipped files Also in general when using more than one file of reference sequences there is no need to concatenate the files into one file as MALT can process multiple files The program malt build will be used to build an index for viral reference sequences We will write the index directory to a directory called index In the parent directory of the references directory run malt build as follows set MALT lt path to malt directory gt malt build i references
13. and use of MALT requires a valid MEGANS license If MEGANS is installed then MALT will locate and use the corresponding license There are a couple of other options random Use to specify the seed used by the random number generator verbose Use to run program in verbose mode help Report command line usage SYNOPSIS MaltBuild options DESCRIPTION Builds the MALT index OPTIONS Input and output i input string s Input reference file s Mandatory option s sequenceType string Sequence type Mandatory option Legal values DNA Protein d index string Name of index directory Mandatory option Performance t threads number Number of worker threads Default value 8 st step number Step size used to advance seed values greater than 1 reduce index size and sensitivity Default value 1 Seed ss shapes string s Seed shape s Default value s default mh maxHitsPerSeed number Maximum number of hits per seed Default value 1000 pr proteinReduct string s Name or definition of protein alphabet reductions one for each seed possible values BLOSUM50_10 BLOSUM50_11 BLOSUM50_15 BLOSUM50_4 BLOSUM50_8 DIAMOND_11 GBMR4 HSDM17 MALT_10 MALT_12A MALT_12B MALT_12C SDM12 UNREDUCED Default value s MALT_12A MALT_12B MALT_12C Classification support g2t gi2taxa string GI to Taxonomy mapping file r2t ref2taxa string RefSeq to Taxonomy mapping file s2t sy
14. e number spr maxSeedsPerRef number sh seedShift number Banded alignment parameters go gapOpen number ge gapExtend number bd band number Properties and license p propertiesFile string Program mode Mandatory option Legal values BlastN BlastP BlastX Type of alignment to be performed Default value Local Legal values Local SemiGlobal Input file s containing queries in FastA or FastQ format Mandatory option Index directory as generated by MaltBuild Mandatory option Output RMA file s or directory Output alignment file s or directory or STDOUT Alignment output format Default value SAM Legal values SAM Tab Text Compress alignments using gzip Default value true Place SQ lines in SAM files Default value false Use soft clipping in SAM files BlastN mode only Default value false Aligned reads output file s or directory or STDOUT Compress aligned reads output using gzip Default value true Unaligned reads output file s or directory or STDOUT Compress unaligned reads output using gzip Default value true Number of worker threads Default value 8 Set the maximum number of seed tables to use O all Default value 0 Cache results for replicated queries Default value false Minimum bit score Default value 50 0 Maximum expected score Default value 1 0 Minimum percent identity Default value 0 0 Maximum number of alignments per query Default value
15. fault value 1 0 minPercentIdentity Minimum percent identity Default value 0 0 maxAlignmentsPerQuery Maximum number of alignments per query Default value 100 maxAlignmentsPerRef Maximum number of non overlapping alignments per reference Default value 1 MALT reports up to this many best scoring matches for each hit reference sequence There are a number of options that are specific to the BlastN mode They are used to specify scoring and are also used in the computation of expected values matchScore Use to specify the alignment match score Default value 2 mismatchScore Use to specify the alignment mis match score Default value 3 setLambda Parameter Lambda for BLASTN statistics Default value 0 625 setK Parameter K for BLASTN statistics Default value 0 41 For BlastP mode and BlastX mode the user need only specify a substitution matrix The Lambda and K values are set automatically subMatrix Use to specify the protein substitution matrix to use Default value BLOSUM62 Legal values BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM90 If the query sequences are DNA or RNA sequences that is if the program is running in BlastN mode or BlastX mode then the following options are available forwardOnly Use to align query forward strand only Default value false reverseOnly Use to align query reverse strand only Default value false The program uses the LCA algorithm 3 to assign reads to
16. he program in this case BlastX Use at to specify the alignment type The option om is used to specify the output directory for matches Here we specify the current directory The option tax requests that a taxonomic analysis of the reads be performed and om requests that the resulting MEGAN file be written to the current directory The file option t specifies the maximum number of threads 3 Obtaining and Installing the Program MALT is written in Java and requires a 64 bit Java runtime environment version 7 or latter freely available from http www java org The Windows and MacOS X installers contain a suitable Java runtime environment that will be used if a suitable Java runtime environment cannot be found on the computer MALT is currently in open alpha testing and is available from http www ab informatik uni tuebingen de software malt There are three different installers that target major operating systems e MALT windows x64_0 1 2 exe provides an installer for Windows e MALT macos_0 1 2 dmg provides an installer for MacOS X e MALT_unix_0 1 2 sh provides an installer for Linux and Unix Download the installer that is appropriate for your computer Please note that the memory re quirement of MALT grows dramatically with the size of the reference database that you wish to employ For example to align sequences against the NR database requires that you have 512GB of main memory Double click on the downloaded i
17. icense 6 Evaluation license 6 gzip 6 hardware requirements 2 15 K parameter 11 Lambda parameter 11 licenseFile 8 12 Linux 5 Local 9 local alignment 9 MacOS X 5 malt build 5 6 malt build gui 5 malt run 5 9 malt run gui 5 malt data cog map gz 8 malt data ncbi map gz 8 malt data ncbi tre gz 8 MALT _macos_0 1 2 dmg 5 MALT _unix_0 1 2 sh 5 MALT_windows x64_0 1 2 exe 5 MEGAN 7 MEGAN alignment tool 1 MEGenome Analyzer 1 memory requirement 5 min support 11 non interactive installation 5 Protein 6 RNA 6 SAM 10 semi global alignment 10 SemiGlobal 10 Single user license 6 Site license 6 SSURef_NR99_115_tax_silva fasta 2 STDOUT 10 synonyms 7 Tab 10 Text 10 top percent 11 Unix 5 vmoptions 5 Windows 5 16
18. ll locate and use the corresponding license The are a couple of other options maxShapes Specify the maximum number of seed shapes to use Only useful if the employed index was built using more than one seed shape By default all seed shapes are used verbose Use to run program in verbose mode help Report command line usage 12 SYNOPSIS MaltRun options DESCRIPTION Runs the MEGAN alignment tool OPTIONS Mode m mode string at alignmentType string Input i inFile string s d index string Output o output string s a alignments string s f format string za gzipAlignments ssq samSQ ssc samSoftClip oa outAligned string s zal gzipAligned ou outUnaligned string s zul gzipUnaligned Performance t numThreads number mt maxTables number rqc replicateQueryCache Filter b minBitScore number e maxExpected number id minPercentIdentity number mq maxAlignmentsPerQuery number mrf maxAlignmentsPerRef number BlastN parameters ma matchScore number mm mismatchScore number la setLambda number K setK number BlastP and BlastX parameters psm subMatrix string DNA query parameters fo forwardOnly ro reverseOnly LCA top topPercent number supp minSupportPercent number sup minSupport number Heuristics spf maxSeedsPerFram
19. malt build There is a number of options for specifying the output generated by the program output Use to specify the names or locations of the output RMA files If a single directory is specified then one output file per input file is written to the specified directory Alternatively if one or more output files are named then the number of output files must equal the number of input files in which case the output for the first input file is written to first output file etc alignments Use to specify the files to which alignments should be written If a single directory is specified then one output file per input file is written to the specified directory Alternatively if one or more output files are named then the number of output files must equal the number of input files in which case the output for the first input file is written to first output file etc If the argument is the special value STDOUT then output is written to standard output rather than to a file If this option is not supplied then the program will not output any matches format Determines the format used to report alignments The default format is SAM Other choices are Text full text BLAST matches and Tab tabulated BLAST format gzipOutput Use this to specify whether alignment output should be gzipped Default is true outAligned Use this to specify that all reads that have at least one significant alignment to some reference sequence should be saved
20. n2taxa string Synonyms to Taxonomy mapping file g2k gi2kegg string GI to KEGG mapping file r2k ref2kegg string RefSeq to KEGG mapping file s2k syn2kegg string Synonyms to KEGG mapping file g2s gi2seed string GI to SEED mapping file r2s ref2seed string RefSeq to SEED mapping file s2s syn2seed string Synonyms to SEED mapping file g2c gi2cog string GI to COG mapping file r2c ref2cog string RefSeq to COG mapping file s2c syn2cog string Synonyms to COG mapping file gif geneInfoFile string File containing gene information Additional files tre taxTree string NCBI tree file ncbi tre as used by MEGAN map taxMap string NCBI map file ncbi map as used by MEGAN cmf cogMappingFile string COG mapping file cog map file as used by MEGAN Properties and license p propertiesFile string Properties file Default value Users huson Library Preferences Megan def L licenseFile string Specify license file Default value Users huson etc megan5 license txt Other rns random number Random number generator seed Default value 666 hsf hashScaleFactor number Hash table scale factor Default value 0 9 v verbose Echo commandline options and be verbose Default value false h help Show program usage and quit Figure 1 Summary of command line usage of malt build 6 The MALT analyzer In summary the program malt run is used to
21. nstaller program to start the interactive installation dialog Alternatively under Linux change into the directory containing the installer and type MALT_unix_0 1 2 sh This will launch the MALT installer in GUI mode To install the program in non gui console mode type MALT_unix_0 1 2 sh c Finally when updating the installation under Linux one can perform a completely non interactive installation like this quiet mode MALT_unix_0 1 2 sh q The installation dialog will ask how much memory the program may use Please set this variable carefully If the amount needs to be changed after installation then this can be done by editing the files ending on vmoptions in the installation directory Two copies of each of the program malt build and malt run will be installed The two copies named malt build and malt run are intended in non interactive commandline use The two copies named malt build gui and malt run gui provide a very simple GUI interface 4 Licensing MALT is an extension of MEGAN and so any usage of MALT requires a valid MEGAN license The following types of licenses are available for MEGAN e Academic license This license permits use of the software exclusively for academic research publications in academic journals and papers at academic conferences and instruction This type of license is available free of charge from the MEGAN5 website e Single user license This license permits a single user to use the program
22. o specify mapping files to map reference sequences to SEED 10 classes Un fortunately the SEED classification does not assign numerical identifiers to classes As a work around malt build uses the numerical identifiers defined and used by MEGAN 4 The detailed usage of three different options is analogous to above g2c r2c s2c Use to specify mapping files to map reference sequences to COG and NOG 12 11 classes Unfortunately COG s and NOG s do not share the same space of numerical identifiers As a work around malt build uses the numerical identifiers defined and used by MEGAN 4 The detailed usage of three different options is analogous to above gif Use this option specify a gene information file Such a file assigns maps genes to intervals in reference sequences as described below This is usually used when the reference sequences are genomes When using classification support a number of additional files may be necessary taxTree Use to specify the taxonomic tree for example malt data ncbi tre gz taxMap Use to specify the associated map file for example malt data ncbi map gz cogMappingFile Use to specify the COG mapping file for example malt data cog map gz There are two options concerned with properties and licensing propertiesFile Use to specify the program properties file By default MALT uses the same file as MEGANS licenseFile Use to specify a MEGANS license file MALT is an extension of MEGAN5
23. ory efficient protein similarity search tool for next generation sequencing data Bioinformatics 28 1 125 126 2012 14 Index alignmentType 9 alignments 10 band 12 cogMappingFile 8 format 10 forwardOnly 11 gapExtend 12 gapOpen 12 gzipAligned 10 gzipOutput 10 help 8 12 inFile 10 index 6 10 input 6 matchScore 11 maxAlignmentsPerQuery 11 maxExpected 11 maxHitsPerSeed 7 maxSeedsPerFrame 12 maxSeedsPerRef 12 maxShapes 12 maxTables 10 minBitPre 12 minBitScore 11 minPercentIdentity 11 minSupport 11 mismatchScore 11 mode 9 outAligned 10 out Unaligned 10 output 10 propertiesFile 8 12 proteinReduct 7 random 8 replicateQueryCache 10 sequenceType 6 setK 11 setLambda 11 shapes 7 step 7 subMatrix 11 taxMap 8 taxTree 8 threads 6 10 topPercent 11 verbose 8 12 g2c 7 g2k 7 g2s 7 g2t 7 gif 7 r2c 7 r2k 7 r2s 7 r2t 7 s2c 7 s2k 7 s2s 7 s2t 7 gz 6 10 gzipUnaligned 10 maxAlignmentsPerRef 11 reverseOnly 11 seedShift 12 xDrop 12 Academic license 6 BlastN mode 9 BLASTN statistics 11 BlastP mode 9 BlastX mode 9 BLOSUM45 11 BLOSUMB0 11 BLOSUM50 8 7 BLOSUM62 11 BLOSUMB0 11 BLOSUMQ0 11 default seed shape 7 Disclaimer 1 DNA 6 Enterprise l
24. reference sequences The malt build program is controlled by command line options as summarized in Figure 1 There are three options for determining input and output input Use to specify all files that contains reference sequences The files must be in FastA format and may be gzipped in which case they must end on gz sequenceType Use to specify whether the reference sequences are DNA or Protein sequences For RNA sequences use the DNA setting index Use to specify the name of the index directory If the directory does not already exist then it will be created If it already exists then any previous index files will be overwritten There are two performance related options threads Use to set the number of threads to use in parallel computations Default is 8 Set this to the number of available cores step Use to set step size used to advance seed values greater than 1 reduce index size and sensitivity Default value 1 The most important performance related option is the maximum amount of memory that malt build is allowed to use This cannot be set from within the program but rather is set during installation of the software MALT uses a seed and extend approach based on spaced seeds 1 7 The following options control this shapes Use this to specify the seed shapes used For DNA sequences the default seed shape is 111110111011110110111111 For protein sequences by default the program uses the fol
25. taxa There are a number of options that control this topPercent Use to specify the top percent value for LCA algorithm Default value is 10 For each read only those matches are used for taxonomic placement whose bit score is within 10 of the best score for that read minSupport Use to specify the min support value for the LCA algorithm 11 There are a number of options that control the heuristics used by malt run maxSeedsPerFrame Maximum number of seed matches per offset per read frame Default value 100 maxSeedsPerRef Maximum number of seed matches per read and reference Default value 20 seedShift Seed shift Default value 1 xDrop XDrop parameter used for ungapped pre screen Default value 7 minBitPre Min bit score used for ungapped pre screen Default value 30 0 The program uses a banded aligner as described in 2 There are a number of associated options gapOpen Use this to specify the gap open penalty Default value 7 gapExtend Use this to specify gap extension penalty Default value 3 band Use this to specify width 2 for banded alignment Default value 4 There are two options concerned with properties and licensing propertiesFile Use to specify the program properties file By default MALT uses the same file as MEGANS licenseFile Use to specify a MEGANS license file MALT is an extension of MEGAN5 and use of MALT requires a valid MEGANS license If MEGANS is installed then MALT wi
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