SortMeRNA User Manual
Contents
1. Gumbel lambda 0 612228 Gumbel K 0 334926 Minimal SW score based on E value 52 Index index silva euk 28s Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 612068 Gumbel K 0 344763 Minimal SW score based on E value 53 Index index rfam 5s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 13 Gumbel lambda 0 616617 Gumbel K 0 341306 Minimal SW score based on E value 51 Index index rfam 5 8s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 617817 Gumbel K 0 340589 Minimal SW score based on E value 49 Number of seeds 2 Edges 4 as integer SW match 2 SW mismatch 3 SW gap open penalty 5 SW gap extend penalty SW ambiguous nucleotide SQ tags are not output Number of threads 1 Reads file SRR106861 fasta H I w Results Total reads 113128 Total reads passing E value threshold 104243 92 15 Total reads failing E value threshold 8885 7 85 Minimum read length 59 Maximum read length 1253 Mean read length 267 By database rRNA_databases silva bac 16s id90 fasta 25 73 rRNA databases silva bac 23s id98 fasta 64 37 rRNA databases silva arc 16s id95 fasta 0 00 rRNA databases silva arc 23s id98 fasta 0 00 rRNA databases silva euk 18s id95 fasta 0 00 rRNA databases silva euk 28s id98 fasta 0 00 rRNA databases rfam 5s database id98 fasta 2 04 rRNA databases rfam 5 8s database id98 f2. classified as significant based on the E value cutoff default 1 SortMeRNA s E value takes into consideration the full size of the reference database as well as the query file thus the E value is higher than BLAST s ex equivalent to BLAST s le 5 gt gt sortmerna ref 97_otus_gg_13_8 fasta index 97_otus_gg_13_8N reads SRR106861 fasta blast 3 sam log aligned SRR106861 gg rRNA a 20 v Program SortMeRNA version 2 0 29 11 2014 Copyright 2012 2015 Bonsai Bioinformatics Research Group LIFL University Lille 1 CNRS UMR 8022 INRIA Nord Europe OTU picking extensions and continuing support developed in the Knight Lab BioFrontiers Institute University of Colorado at Boulder Disclaimer SortMeRNA comes with ABSOLUTELY NO WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details Contact Evguenia Kopylova jenya kopylov gmail com Laurent Noe laurent noe lifl fr Helene Touzet helene touzet lifl fr Computing read file statistics done 0 44 sec size of reads file 35238748 bytes partial section s to be executed 1 of size 35238748 bytes Parameters summary Number of seeds 2 Edges 4 as integer SW match 2 SW mismatch 3 SW gap open penalty 5 SW gap extend penalty SW ambiguous nucleotide SQ tags are not output Number of threads 20 2 3 Begin mmap reads section 1 Time to mmap reads and s
3. parameters for filtering and read mapping In SortMeRNA version 1 99 beta and up users have the option to output sequence alignments for their matching rRNA reads in the SAM or BLAST like formats Depending on the desired quality of alignments different parameters choices must be set Table 1 presents a guide to setting parameters choices for most use cases In all cases output alignments are always guaranteed to reach the threshold E value score default E value 1 An E value of 1 signifies that one random alignment is expected for aligning all reads against the reference database The E value in SortMeRNA is computed for the entire search space not per read Table 1 SortMeRNA alignment parameter guide option speed description Output the first alignment passing E value Very fast for INT 1 threshold best choice if only filtering is needed Speed decreases for higher value INT Higher INT signifies more alignments will be num alignments INT made amp output All alignments reaching the E value threshold are reported this option is not suggested for Very slow for INT 0 high similarity rRNA databases due to many possible alignments per read causing a very large file output Only one high candidate reference sequence will be searched for alignments determined Fast for INT 1 heuristically using a Longest Increasing Sub sequence of seed matches The single best Sore ae alignment of those will be reported Hig
4. sortmerna 2 4 Uninstall If the user installed SortMeRNA using the command make install then they can use the com mand make uninstall to uninstall SortMeRNA with root permissions 3 Databases SortMeRNA comes prepackaged with 8 databases representative database seq clustered origin seq original silva bac 16s id90 silva arc 16s id95 silva euk 18s id95 silva bac 23s id98 silva arc 23s id98 silva euk 28s id98 rfam 5s id98 rfam 5 8s id98 12798 3193 7348 4488 251 4935 59513 13034 SILVA SSU Ref NR v 119 SILVA SSU Ref NR v 119 SILVA SSU Ref NR v 119 SILVA LSU Ref v 119 SILVA LSU Ref v 119 SILVA LSU Ref v 119 RFAM RFAM 464618 18797 51553 43822 629 13095 116760 225185 HMMER 3 1b1 and SumaClust v1 0 00 were used to reduce the size of the original databases to the similarity listed in column 2 id of the table above see sortmerna rRNA databases README txt for a list of complete steps These representative databases were specifically made for fast filtering of rRNA Approximately the same number of rRNA will be filtered using silva bac 16s id90 12802 rRNA as using Greengenes 97 99322 rRNA but the former will run significantly faster id members of the cluster must have identity at least this id with the representative sequence Remark The user must first index the fasta database by using the command indexdb_rna and then filter map reads agains
5. the aligned and other files possibly breaking the order for a set of paired reads between two output files It s important to note that regardless of the options used the log file will always report the true number of reads classified as rRNA not the number of reads in the aligned file 4 3 3 Example 4 forward reverse paired end reads 2 input files FASTQ forward reads GSEQUENCE ID_1 1 ACTT QUALITY_1 1 SEQUENCE_ID 2 1 GTTA QUALITY 2 1 pair 1 pair 2 FASTQ reverse reads GSEQUENCE ID_1 2 GTAC QUALITY 1 2 SE UENCE ID 2 2 CCAC QUALITY 2 2 Figure 2 Forward and reverse reads in paired end sequencing format FASTQ paired end reads GSEQUENCE ID_1 1 ACTT QUALITY 1 1 SEQUENCE_ID_1 2 GTAC QUALITY 1 2 Figure 3 Paired end read format accepted by SortMeRNA SortMeRNA accepts only 1 file as input for the reads If a user has two input files in the case for the foward and reverse paired end reads see Figure 2 they may use the merge paired reads sh script found in sortmerna scripts folder to interleave the paired reads into the format of Fig ure 3 The command for merge paired reads sh is the following gt bash merge paired reads sh forward reads fastq reverse reads fastq outfile fastq 15 Now the user may input outfile fastq to SortMeRNA for analysis Similarly for unmerging the paired reads back into two separate f
6. 5 71 18 4 5 OTU picking SortMeRNA is implemented in QIIME s closed reference and open reference OTU picking work flows The readers are referred to IIME s tutorials for an in depth discussion of these methods http qiime org tutorials otu_picking html 5 SortMeRNA advanced options num_seeds INT The threshold number of seeds required to match in the primary seed search filter before moving on to the secondary seed cluster filter More specifically the threshold number of seeds required before searching for a longest increasing subsequence LIS of the seeds positions between the read and the closest matching reference sequence By default this is set to 2 seeds passes INT INT INT In the primary seed search filter SortMeRNA moves a seed of length Z parameter of indexdb_rna across the read using three passes If at the end of each pass a threshold number of seeds defined by num seeds did not match to the reference database SortMeRNA attempts to find more seeds by decreasing the interval at which the seed is placed along the read by using another pass In default mode these intervals are set to L L 2 3 for Pass 1 2 and 3 respectively Usually if the read is highly similar to the reference database a threshold number of seeds will be found in the first pass edges INT The number or percentage if followed by of nucleotides to add to each edge of the alignment region on the reference sequence before per
7. Citation 20 1 Introduction Copyright C 2012 2015 Bonsai Bioinformatics Research Group LIFL Universit Lille 1 CNRS UMR 8022 INRIA Nord Europe http bioinfo lifl fr RNA sortmerna OTU picking extensions and continuous support developed in the Knight Lab BioFrontiers Institute University of Colorado at Boulder CO https knightlab colorado edu SortMeRNA is a local sequence alignment tool for filtering mapping and OTU picking The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of NGS reads The main application of SortMeRNA is filtering rRNA from metatranscriptomic data Addi tional applications include OTU picking and taxonomy assignation available through QIIME v1 9 http qiime org currently the development version to be released in early December Sort MeRNA takes as input a file of reads fasta or fastq format and one or multiple rRNA database file s and sorts apart aligned and rejected reads into two files specified by the user SortMeRNA works with Illumina 454 Ion Torrent and PacBio data and can produce SAM and BLAST like alignments For questions amp help please contact 1 Evguenia Kopylova evguenia kopylova lifl fr 2 Laurent Noe laurent noe lifl fr 3 Helene Touzet helene touzet lifl fr Important This user manual is strictly for SortMeRNA version 2 0 2 Installation 2 1 Install from tarball release 1 Download sortmerna 2 0 tar gz from https github c
8. NT the amount of memory in Mbytes for building the index 3072 L INT seed length 18 max pos INT maximum number of positions to store for each unigue L mer 10000 setting max pos 0 will store all positions v BOOL verbose h BOOL help There are eight rRNA representative databases provided in the sortmerna 2 0 rRNA_databases folder All databases were derived from the SILVA SSU and LSU databases release 119 and the RFAM databases using HMMER 3 1b1 and SumaClust v1 0 00 Additionally the user can index their own database 4 1 1 Example 1 indexdb_rna using one database gt gt indexdb_rna ref rRNA_databases silva bac 16s id90 fasta index silva bac 16s db v Program SortMeRNA version 2 0 29 11 2014 Copyright 2012 2015 Bonsai Bioinformatics Research Group LIFL University Lille 1 CNRS UMR 8022 INRIA Nord Europe OTU picking extensions and continuing support developed in the Knight Lab BioFrontiers Institute University of Colorado at Boulder Disclaimer SortMeRNA comes with ABSOLUTELY NO WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details Contact Evguenia Kopylova jenya kopylov gmail com Laurent Noe laurent noe lifl fr Helene Touzet helene touzet lifl fr Parameters summary K mer size 19 K mer interval 1 Maximum positions to store per unique K mer 10000 Total number of databases to index 1 Beg
9. SortMeRNA User Manual Evguenia Kopylova jenya kopylovQgmail com Oct 2014 version 2 0 Contents 1 2 Introduction 3 Installation 3 2 1 Install from tarball release on 3 2 2 Install development version from git 0 0 00 LL 4 2 3 Install from precompiled code 2 0 0 0 02 ee ee 4 2 4 Wninstall bce ge wk Rd BO TA APE a EE oe hE ee a PR dd ad 5 Databases 5 How to run SortMeRNA 5 4 1 Index the rRNA database command indexdb_rna 0 5 4 1 1 Example 1 indexdb rna using one database 144111 6 7 8 4 1 2 Example 2 indexdb_rna using multiple databases 1 4 2 A guide to choosing sortmerna parameters for filtering and read mapping 430 Ber tRNA reads 5 dE kan ae eU Pp od Es NUK A ite ok BE AA 9 4 3 1 Example 3 multiple databases and the fastest alignment option 11 4 3 2 Filtering paired end reads 4 Qu LL LL LL Le 14 4 3 3 Example 4 forward reverse paired end reads 2 input files 15 AA Read mapping qe E TAT R da PE RR a DR T A A 17 4 4 1 Mapping reads for classification ooo e LL Le 17 4 4 2 Example 5 mapping reads against the 16S Greengenes 97 id database with multithreading we 1 6 hace i rai e Ge a ee aa AN EN Gay dte e Ll 17 A9 ONU PCI OS 2 R e 4 Gee owa ob oe Ee ee Ba eke Bit nia da P A oaa 19 SortMeRNA advanced options 19 Help 20
10. asta 0 00 4 3 2 Filtering paired end reads When writing aligned and non aligned reads to FASTA Q files sometimes the situation arises where one of the paired end reads aligns and the other one doesn t Since SortMeRNA looks at each read individually by default the reads will be split into two separate files That is the read that aligned will go into the aligned FASTA Q file and the pair that didn t align will go into the other FASTA Q file This situation would result in the splitting of some paired reads in the output files and not optimal for users who require paired order of the reads for downstream analyses For users who wish to keep the order of their paired ended reads two options are available If one read aligns and the other one not then 1 paired in will put both reads into the file specified by aligned 2 paired out will put both reads into the file specified by other The first option paired in is optimal for users that want all reads in the other file to be non rRNA However there are small chances that reads which are non rRNA will also be put into the aligned file 14 The second option paired out is optimal for users that want only rRNA reads in the aligned file However there are small chances that reads which are rRNA will also be put into the other file If neither of these two options is added to the sortmerna command then aligned and non aligned reads will be properly output to
11. e mandatory appropriate extension will be added COMMON OPTIONS other STRING rejected reads filepath base file name appropriate extension will be added fastx BOOL output FASTA FASTQ file off for aligned and or rejected reads sam BOOL output SAM alignment off for aligned reads only SQ BOOL add SQ tags to the SAM file off blast INT output alignments in various Blast like formats 0 pairwise 1 tabular Blast m 8 format 2 tabular column for CIGAR 3 tabular columns for CIGAR and query coverage log BOOL output overall statistics off num_alignments INT report first INT alignments per read reaching E value cil num_alignments O signifies all alignments will be output or default best min_lis INT report INT best alignments per read reaching E value 1 by searching min_lis INT candidate alignments best 0 signifies all candidate alignments will be searched INT search all alignments having the first INT longest LIS 2 LIS stands for Longest Increasing Subsequence it is computed using seeds positions to expand hits into longer matches prior to Smith Waterman alignment print_all_reads BOOL output null alignment strings for non aligned reads off to SAM and or BLAST tabular files paired_in BOOL paired_out BOOL match INT mismatch INT gap_open INT gap_ext INT N INT F BOOL R BOOL a INT e DOUBLE m INT v BOOL OTU PICKING OPTIONS id DOUBLE covera
12. et up pointers 0 10 sec 17 Begin analysis of 97_otus_gg_13_8 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 600470 Gumbel K 0 327880 Minimal SW score based on E value 57 Loading index part 1 1 done 10 76 sec Begin index search done 23 75 sec Freeing index done 1 44 sec Total number of reads mapped incl all reads file sections searched 29089 Writing alignments done 7 71 sec This is almost the same number of 165 rRNA as identified by SortMeRNA using the smaller provided database gt gt cat SRR106861_gg_rRNA log Date and time Command sortmerna ref 97_otus_gg_13_8 fasta index 97_otus_gg_13_8 reads SRR106861 fasta blast 3 sam log aligned SRR106861 gg rRNA a 20 v Process pid 44246 Parameters summary Index index 97_otus_gg_13_8 Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 600470 Gumbel K 0 327880 Minimal SW score based on E value 57 Number of seeds 2 Edges 4 as integer SW match 2 SW mismatch 3 SW gap open penalty 5 SW gap extend penalty 2 SW ambiguous nucleotide SQ tags are not output Number of threads 20 Reads file SRR106861 fasta 3 Results Total reads 113128 Total reads passing E value threshold 29089 25 71 Total reads failing E value threshold 84039 74 29 Minimum read length 59 Maximum read length 1253 Mean read length 267 By database 97_otus_gg_13_8 fasta 2
13. forming Smith Waterman alignment By default this is set to 4 nucleotides full_search FLAG During the index traversal if a seed match is found with 0 errors SortMeRNA will stop searching for further l error matches This heuristic is based upon the assumption that 0 error matches are more significant than 1 error matches By turning it off using the full_search flag the sensitivity may increase often by less than 1 but with up to four fold decrease in speed pid FLAG The pid of the running sortmerna process will be added to the output files in order to avoid over writing output if the same aligned STRING base name is provided for different runs 19 6 Help Any issues or bug reports should be reported to https github com biocore sortmerna issues or by e mail to the authors see list of e mails in Section 1 of this document Comments and suggestions are also always appreciated 7 Citation If you use SortMeRNA please cite Kopylova E No L and Touzet H SortMeRNA Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Bioinformatics 2012 doi 10 1093 bioinformatics bts611 20
14. ge DOUBLE de_novo_otu BOOL otu_map BOOL both paired end reads go in aligned fasta q file interleaved reads only see Section 4 2 4 of User Manual both paired end reads go in other fasta q file interleaved reads only see Section 4 2 4 of User Manual SW score positive integer for a match SW penalty negative integer for a mismatch SW penalty positive integer for introducing a gap SW penalty positive integer for extending a gap SW penalty for ambiguous letters N s search only the forward strand search only the reverse complementary strand number of threads to use E value threshold INT Mbytes for loading the reads into memory maximum m INT is 4096 verbose hid similarity threshold the alignment must still pass the E value threshold query coverage threshold the alignment must still pass the E value threshold FASTA FASTQ file for reads matching database lt id set using id and lt cov set using coverage alignment must still pass the E value threshold output OTU map input to QIIME s make_otu_table py ADVANCED OPTIONS see SortMeRNA user manual for more details passes edges INT num_seeds INT full_search BOOL pid BOOL HELP h BOOL version BOOL The user can adjust the amount of memory allocated for loading the reads through the command option m By default m is set to be high enough for 1GB If the reads file is larger than 1GB then sortmerna internal
15. her INT signifies more alignments will be Speed decreases for higher value INT made though only the best one will be re ported All high candidate reference sequences will be Very slow for INT 0 searched for alignments though only the best one will be reported 4 3 Filter rRNA reads The executable sortmerna can filter rRNA reads against an indexed rRNA database To see the man page for sortmerna gt gt sortmerna h Program Copyright Disclaimer Contact reads aligned SortMeRNA version 2 0 29 11 2014 2012 2015 Bonsai Bioinformatics Research Group LIFL University Lille 1 CNRS UMR 8022 INRIA Nord Europe OTU picking extensions and continuing support developed in the Knight Lab BioFrontiers Institute University of Colorado at Boulder SortMeRNA comes with ABSOLUTELY NO WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details Evguenia Kopylova jenya kopylov gmail com Laurent Noe laurent noe lifl fr Helene Touzet helene touzet lifl fr STRING STRING FASTA reference file index file mandatory ex ref path to file1 fasta path to index1 If passing multiple reference files separate them using the delimiter ex ref path to file1 fasta path to index1 path to file2 fasta path to index STRING FASTA FASTQ reads file mandatory STRING aligned reads filepath base file nam
16. iles use the command gt bash unmerge paired reads sh merged reads fastq forward reads fastq reverse reads fastq Important unmerge paired reads sh should only be used if one of the options paired_in or paired_out was used during filtering Otherwise it may give incorrect results if a paired read was split during alignment one read aligned and the other one not 16 4 4 Read mapping 4 4 1 Mapping reads for classification Although SortMeRNA is very sensitive with the small rRNA databases distributed with the source code these databases are not optimal for classification since often alignments with 75 90 identity will be returned there are only several thousand rRNA in most of the databases compared to the original SILVA or Greengenes databases containing millions of rRNA Classification at the species level generally considers alignments at 97 and above so it is suggested to use a larger database is species classification is the main goal Moreover SortMeRNA is a local alignment tool so it s also important to look at the query coverage for each alignment In the SAM output format neither id or query coverage are reported If the user wishes for these values then the Blast tabular format with CIGAR query coverage option blast 3 is the way to go 4 4 2 Example 5 mapping reads against the 16S Greengenes 97 id database with multithreading This example will generate SAM and BLAST tabular output files Alignments are
17. in indexing file rRNA_databases silva bac 16s id90 fasta under index name index silva bac 16s db Collecting sequence distribution statistics done 1 133206 sec start index part 0 1 3 building burst tries done 23 643256 sec 2 3 building CMPH hash done 22 306709 sec 3 3 building position lookup tables done 54 958680 sec total number of sequences in this part 12798 writing kmer data to index silva bac 16s db kmer_0 dat writing burst tries to index silva bac 16s db bursttrie_0 dat writing position lookup table to index silva bac 16s db pos_0 dat writing nucleotide distribution statistics to index silva bac 16s db stats done 4 1 2 Example 2 indexdb_rna using multiple databases Multiple databases can be indexed simultaneously by passing them as a no spaces allowed separated list to ref gt gt indexdb_rna ref rRNA databases silva bac 16s id90 fasta index silva bac 16s db N rRNA databases silva bac 23s id98 fasta index silva bac 23s db N rRNA databases silva arc 16s id95 fasta index silva arc 16s db N rRNA databases silva arc 23s id98 fasta index silva arc 23s db N rRNA databases silva euk 18s id95 fasta index silva euk 18s db N rRNA databases silva euk 28s id98 fasta index silva euk 28s N rRNA databases rfam 5s database id98 fasta index rfam 5s db N rRNA_databases rfam 5 8s database id98 fasta index rfam 5 8s db 4 2 A guide to choosing sortmerna
18. index part 1 1 done 3 23 sec Begin index search done 30 28 sec Freeing index done 0 45 sec Begin analysis of rRNA_databases silva euk 28s id98 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 612068 Gumbel K 0 344763 Minimal SW score based on E value 53 Loading index part 1 1 done 3 43 sec Begin index search done 35 69 sec Freeing index done 0 48 sec Begin analysis of rRNA_databases rfam 5s database id98 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 616617 Gumbel K 0 341306 Minimal SW score based on E value 51 Loading index part 1 1 done 1 77 sec Begin index search done 13 50 sec Freeing index done 0 22 sec Begin analysis of rRNA_databases rfam 5 8s database id98 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 617817 Gumbel K 0 340589 Minimal SW score based on E value 49 Loading index part 1 1 done 0 60 sec Begin index search done 8 78 sec Freeing index done 0 07 sec Total number of reads mapped incl all reads file sections searched 104243 12 Writing aligned FASTA FASTQ done 1 13 sec Writing not aligned FASTA FASTQ done 0 10 sec The option log will create an overall statistics file gt gt cat SRR105861 rRNA log Time and date Command sortmerna ref rRNA databases silva bac 16s id90 fasta index silva bac 16
19. ly divides the file into partial sections of 1GB and executes one section at a time Hence if a user has an input file of 15GB and only 1GB of RAM to store it the file will be processed in partial sections using mmap without having to physically split it prior to execution Otherwise the user can increase m to map larger portions of the file The limit for m is given by typing sortmerna h INT INT INT three intervals at which to place the seed on the read L is the seed length set in indexdb_rna number or percent if INT followed by sign of nucleotides to add to each edge of the read prior to SW local alignment number of seeds matched before searching for candidate LIS search for all O error and 1 error seed matches in the index rather than stopping after finding a O error match lt 1 gain in sensitivity with up four fold decrease in speed add pid to output file names help SortMeRNA version number 10 off off scored as mismatch off off 1 1 1024 off off off L L 2 3 off off 4 3 1 Example 3 multiple databases and the fastest alignment option gt gt time sortmerna ref rRNA_databases silva bac 16s id90 fasta index silva bac 16s db N rRNA databases silva bac 23s id98 fasta index silva bac 23s db N rRNA databases silva arc 16s id95 fasta index silva arc 16s db N rRNA databases silva arc 23s id98 fasta index silva arc 23s db N rRNA databases silva euk 18s id95 fa
20. om biocore sortmerna releases 2 Extract the source code package into a directory of your choice enter sortmerna 2 0 directory and type gt bash build sh 3 At this point two executables indexdb_rna and sortmerna will be located in the sortmerna 2 0 directory If the user would like to install the executables into their default installation direc tory usr local bin for Linux or opt local bin for Mac then type gt make install with root permissions 4 To begin using SortMeRNA type indexdb_rna h or sortmerna h Databases must first be indexed using indexdb_rna Figure 1 sortmerna 2 0 directory tree sortmerna 2 0 he cmph include scripts 38 w D n T ot n rRNA_databases silva bac 16s id90 fasta sortmerna i indexdb_rna 2 2 Install development version from git 1 Clone the sortmerna directory to your local system gt git clone https github com biocore sortmerna git 2 Build sortmerna gt cd sortmerna gt bash build sh 2 3 Install from precompiled code 1 Download the latest binary distribution of SortMeRNA from http bioinfo lifl fr RNA sortmerna 2 Extract the source code package into a directory of your choice gt tar xvf sortmerna 2 0 tar gz gt cd sortmerna 2 0 3 To begin using SortMeRNA type indexdb_rna h or sortmerna h The user must firstly index the databases with the command indexdb_rna before they can run the command
21. s db N rRNA databases silva bac 23s id98 fasta index silva bac 23s db N rRNA databases silva arc 16s id95 fasta index silva arc 16s db N rRNA databases silva arc 23s id98 fasta index silva arc 23s db N rRNA databases silva euk 18s id95 fasta index silva euk 18s db N rRNA databases silva euk 28s id98 fasta index silva euk 28s N rRNA_databases rfam 5s database id98 fasta index rfam 5s db N rRNA databases rfam 5 8s database id98 fasta index rfam 5 8s dbN reads Users jenya Downloads SRR106861 fasta sam num alignments 1 fastx aligned SRR105861 rRNA other SRR105861 non rRNA fasta fasta v Process pid 1957 Parameters summary Index index silva bac 16s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 602397 Gumbel K 0 328927 Minimal SW score based on E value 54 Index index silva bac 23s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 603075 Gumbel K 0 330488 Minimal SW score based on E value 53 Index index silva arc 16s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 596230 Gumbel K 0 322143 Minimal SW score based on E value 52 Index index silva arc 23s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 597749 Gumbel K 0 325630 Minimal SW score based on E value 49 Index index silva euk 18s db Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3
22. ses silva bac 16s id90 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 602397 Gumbel K 0 328927 Minimal SW score based on E value 54 Loading index part 1 1 done 4 67 sec Begin index search done 83 53 sec Freeing index done 0 87 sec Begin analysis of rRNA_databases silva bac 23s id98 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 603075 Gumbel K 0 330488 Minimal SW score based on E value 53 Loading index part 1 1 done 3 63 sec Begin index search done 94 76 sec 11 Freeing index done 0 41 sec Begin analysis of rRNA_databases silva arc 16s id95 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 596230 Gumbel K 0 322143 Minimal SW score based on E value 52 Loading index part 1 1 done 1 14 sec Begin index search done 22 63 sec Freeing index done 0 14 sec Begin analysis of rRNA_databases silva arc 23s id98 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 597749 Gumbel K 0 325630 Minimal SW score based on E value 49 Loading index part 1 1 done 0 50 sec Begin index search done 13 27 sec Freeing index done 0 06 sec Begin analysis of rRNA_databases silva euk 18s id95 fasta Seed length 18 Pass 1 18 Pass 2 9 Pass 3 3 Gumbel lambda 0 612228 Gumbel K 0 334926 Minimal SW score based on E value 52 Loading
23. sta index silva euk 18s db N rRNA databases silva euk 28s id98 fasta index silva euk 28s N rRNA databases rfam 5s database id98 fasta index rfam 5s db N rRNA databases rfam 5 8s database id98 fasta index rfam 5 8s dbN reads SRR106861 fasta sam num alignments 1 fastx aligned SRR105861_rRNA other SRR105861 non rRNA log v Program SortMeRNA version 2 0 29 11 2014 Copyright 2012 2015 Bonsai Bioinformatics Research Group LIFL University Lille 1 CNRS UMR 8022 INRIA Nord Europe OTU picking extensions and continuing support developed in the Knight Lab BioFrontiers Institute University of Colorado at Boulder Disclaimer SortMeRNA comes with ABSOLUTELY NO WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details Contact Evguenia Kopylova jenya kopylov gmail com Laurent Noe laurent noe lifl fr Helene Touzet helene touzet lifl fr Computing read file statistics done 2 16 sec size of reads file 35238748 bytes partial section s to be executed 1 of size 35238748 bytes Parameters summary Number of seeds 2 Edges 4 as integer SW match 2 SW mismatch 3 SW gap open penalty 5 SW gap extend penalty SW ambiguous nucleotide SQ tags are not output Number of threads 1 2 3 Begin mmap reads section 1 Time to mmap reads and set up pointers 0 11 sec Begin analysis of rRNA_databa
24. t the database using the command sortmerna 4 How to run SortMeRNA 4 1 Index the rRNA database command indexdb_rna The executable indexdb_rna indexes an rRNA database To see the man page for indexdb_rna gt gt indexdb rna h Program Copyright SortMeRNA version 2 0 29 11 2014 2012 2015 Bonsai Bioinformatics Research Group LIFL University Lille 1 CNRS UMR 8022 INRIA Nord Europe OTU picking extensions and continuing support developed in the Knight Lab BioFrontiers Institute University of Colorado at Boulder Disclaimer SortMeRNA comes with ABSOLUTELY NO WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details Contact Evguenia Kopylova jenya kopylov gmail com Laurent Noe laurent noe lifl fr Helene Touzet helene touzet lifl fr usage indexdb_rna ref db fasta db idx OPTIONS parameter value description default ref STRING STRING FASTA reference file index file mandatory ex ref path to file1 fasta path to index1 If passing multiple reference sequence files separate them by ex ref path to file1 fasta path to index1 path to file2 fasta path to index2 OPTIONS fast BOOL suggested option for aligning 99 related species off sensitive BOOL suggested option for aligning 75 98 related species on tmpdir STRING directory where to write temporary files m I
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