Description

Local sequence alignment tool for filtering, mapping and clustering.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

fastas (file)

Path to reference file(s)

meta3 (map)

Groovy Map containing index information
e.g. [ id:‘test’ ]

index (directory)

Path to index directory of a previous sortmerna run

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

], or reference information from an
indexing-only run

reads (file)

The filtered fastq reads

*fastq.gz

log (file)

SortMeRNA log file

*sortmerna.log

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

index (directory)

Path to index directory generated by sortmern

versions (file)

File containing software versions

versions.yml
included in
denovotranscript riboseq rnaseq
maintainers
Github user drpatelh
Github user mashehu
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

SortMeRNA
GPL-3.0-or-later

The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

hpc.nih.gov/apps/sortmeRNA github.com/biocore/sortmerna/wiki