sortmerna

sort

mRNA

rRNA

alignment

filtering

mapping

clustering

Description

Local sequence alignment tool for filtering, mapping and clustering. The main
application of SortMeRNA is filtering rRNA from metatranscriptomic data.

Input

Name	Type & Properties	Description
--paired	boolean_true	Reads are paired-end. If a single reads file is provided, use this option to indicate the file contains interleaved paired reads when neither 'paired_in' \| 'paired_out' \| 'out2' \| 'sout' are specified.
--input	file multiple	Input fastq
--ref	file multiple	Reference fasta file(s) for rRNA database.
--ribo_database_manifest	file	Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.

Name

Type & Properties

--paired

boolean_true

--input

file

multiple

--ref

file

multiple

--ribo_database_manifest

file

Output

Name	Type & Properties	Description
--log	file output	Sortmerna log file.
--output --aligned	file output	Directory and file prefix for aligned output. The appropriate extension: (fasta\|fastq\|blast\|sam\|etc) is automatically added. If 'dir' is not specified, the output is created in the WORKDIR/out/. If 'pfx' is not specified, the prefix 'aligned' is used.
--other	file output	Create Non-aligned reads output file with this path/prefix. Must be used with fastx.

Name

Type & Properties

--log

file

output

--output

--aligned

file

output

--other

file

output

Options

Name	Type & Properties	Description
--kvdb	string	Path to directory of the key-value database file, used for storing the alignment results.
--idx_dir	string	Path to the directory for storing the reference index files.
--readb	string	Path to the directory for storing pre-processed reads.
--fastx	boolean_true	Output aligned reads into FASTA/FASTQ file
--sam	boolean_true	Output SAM alignment for aligned reads.
--sq	boolean_true	Add SQ tags to the SAM file
--blast	string	Blast options: * '0' - pairwise * '1' - tabular(Blast - m 8 format) * '1 cigar' - tabular + column for CIGAR * '1 cigar qcov' - tabular + columns for CIGAR and query coverage * '1 cigar qcov qstrand' - tabular + columns for CIGAR, query coverage and strand
--num_alignments	integer	Report first INT alignments per read reaching E-value. If Int = 0, all alignments will be output. Default: '0'
--min_lis	integer	search all alignments having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. Default: '2'.
--print_all_reads	boolean_true	output null alignment strings for non-aligned reads to SAM and/or BLAST tabular files.
--paired_in	boolean_true	In the case where a pair of reads is aligned with a score above the threshold, the output of the reads is controlled by the following options: * --paired_in and --paired_out are both false: Only one read per pair is output to the aligned fasta file. * --paired_in is true and --paired_out is false: Both reads of the pair are output to the aligned fasta file. * --paired_in is false and --paired_out is true: Both reads are output the the other fasta file (if it is specified).
--paired_out	boolean_true	See description of --paired_in.
--out2	boolean_true	Output paired reads into separate files. Must be used with '--fastx'. If a single reads file is provided, this options implies interleaved paired reads. When used with 'sout', four (4) output files for aligned reads will be generated: 'aligned-paired-fwd, aligned-paired-rev, aligned-singleton-fwd, aligned-singleton-rev'. If 'other' option is also used, eight (8) output files will be generated.
--sout	boolean_true	Separate paired and singleton aligned reads. Must be used with '--fastx'. If a single reads file is provided, this options implies interleaved paired reads. Cannot be used with '--paired_in' or '--paired_out'.
--zip_out	string	Compress the output files. The possible values are: * '1/true/t/yes/y' * '0/false/f/no/n' *'-1' (the same format as input - default) The values are Not case sensitive.
--match	integer	Smith-Waterman score for a match (positive integer). Default: '2'.
--mismatch	integer	Smith-Waterman penalty for a mismatch (negative integer). Default: '-3'.
--gap_open	integer	Smith-Waterman penalty for introducing a gap (positive integer). Default: '5'.
--gap_ext	integer	Smith-Waterman penalty for extending a gap (positive integer). Default: '2'.
--N	integer	Smith-Waterman penalty for ambiguous letters (N's) scored as --mismatch. Default: '-1'.
--a	integer	Number of threads to use. Default: '1'.
--e	double	E-value threshold. Default: '1'.
--F	boolean_true	Search only the forward strand.
--R	boolean_true	Search only the reverse-complementary strand.
--num_alignment	integer	Report first INT alignments per read reaching E-value (--num_alignments 0 signifies all alignments will be output). Default: '-1'
--best	integer	Report INT best alignments per read reaching E-value by searching --min_lis INT candidate alignments (--best 0 signifies all candidate alignments will be searched) Default: '1'.
--verbose -v	boolean_true	Verbose output.

Name

Type & Properties

--kvdb

string

--idx_dir

string

--readb

string

--fastx

boolean_true

--sam

boolean_true

--sq

boolean_true

--blast

string

--num_alignments

integer

--min_lis

integer

--print_all_reads

boolean_true

--paired_in

boolean_true

--paired_out

boolean_true

--out2

boolean_true

--sout

boolean_true

--zip_out

string

--match

integer

--mismatch

integer

--gap_open

integer

--gap_ext

integer

--N

integer

--a

integer

--e

double

--F

boolean_true

--R

boolean_true

--num_alignment

integer

--best

integer

--verbose

-v

boolean_true

OTU picking options

Name	Type & Properties	Description
--id	double	%id similarity threshold (the alignment must still pass the E-value threshold). Default: '0.97'.
--coverage	double	%query coverage threshold (the alignment must still pass the E-value threshold). Default: '0.97'.
--de_novo	boolean_true	FASTA/FASTQ file for reads matching database < %id off (set using --id) and < %cov (set using --coverage) (alignment must still pass the E-value threshold).
--otu_map	boolean_true	Output OTU map (input to QIIME's make_otu_table.py).

Name

Type & Properties

--id

double

--coverage

double

--de_novo

boolean_true

--otu_map

boolean_true

Advanced options

Name	Type & Properties	Description
--num_seed	integer	Number of seeds matched before searching for candidate LIS. Default: '2'.
--passes	integer multiple	Three intervals at which to place the seed on the read L,L/2,3 (L is the seed length set in ./indexdb_rna).
--edge	string	The number (or percentage if followed by %) of nucleotides to add to each edge of the alignment region on the reference sequence before performing Smith-Waterman alignment. Default: '4'.
--full_search	boolean_true	Search for all 0-error and 1-error seed off matches in the index rather than stopping after finding a 0-error match (<1% gain in sensitivity with up four-fold decrease in speed).

Name

Type & Properties

--num_seed

integer

--passes

integer

multiple

--edge

string

--full_search

boolean_true

Indexing Options

Name	Type & Properties	Description
--index	integer	Create index files for the reference database. By default when this option is not used, the program checks the reference index and builds it if not already existing. This can be changed by using '-index' as follows: * '-index 0' - skip indexing. If the index does not exist, the program will terminate and warn to build the index prior performing the alignment * '-index 1' - only perform the indexing and terminate * '-index 2' - the default behaviour, the same as when not using this option at all
-L	double	Indexing seed length. Default: '18'
--interval	integer	Index every Nth L-mer in the reference database. Default: '1'
--max_pos	integer	Maximum number of positions to store for each unique L-mer. Set to 0 to store all positions. Default: '1000'

Name

Type & Properties

--index

integer

-L

double

--interval

integer

--max_pos

integer

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
log: "$id.$key.log.log"  
output: "$id.$key.output"  
other: "$id.$key.other"  
id: .nan  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/sortmerna/main.nf \  
  -params-file params.yaml

sortmerna

Input

Output

Options

OTU picking options

Advanced options

Indexing Options

Run this component

Relationships

Used by

Uses