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SortMeRNA: next-generation sequence filtering and alignment tool

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sortmerna

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SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.

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. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

SortMeRNA is also available through QIIME v1.9.1 and the nf-core RNA-Seq pipeline v.3.9.

Table of Contents

Getting Started

SortMeRNA 4 is C++17 compliant, and mostly uses standard libraries. It uses CMake as the build system, and can be run/built on all major OS including Linux, Windows, and Mac.

Using Conda package

conda config --add channels bioconda

conda search sortmerna
  Loading channels: done
  # Name                       Version           Build  Channel
  sortmerna                        2.0               0  bioconda
  ...
  sortmerna                      4.3.4               0  bioconda
  ...
  sortmerna                      4.3.6               0  bioconda

conda install sortmerna
which sortmerna
  /home/biocodz/miniconda3/bin/conda

# test the installation
sortmerna --version
  SortMeRNA version 4.3.6
  Build Date: Aug 16 2021
  sortmerna_build_git_sha:@921fa40256760ea2d44c49b21eb326afda748d5e@
  sortmerna_build_git_date:@2022/08/16 10:59:31@

# view help
sortmerna -h

Using GitHub release binaries on Linux

Visit Sortmerna GitHub Releases

Linux distribution is a Shell script with the embedded installation archive.

Issue the following bash commands:

pushd ~

# get the distro
wget https://github.com/biocore/sortmerna/releases/download/v4.3.6/sortmerna-4.3.6-Linux.sh

# view the installer usage
bash sortmerna-4.3.6-Linux.sh --help
    Options: [defaults in brackets after descriptions]
      --help            print this message
      --version         print cmake installer version
      --prefix=dir      directory in which to install
      --include-subdir  include the sortmerna-4.3.6-Linux subdirectory
      --exclude-subdir  exclude the sortmerna-4.3.6-Linux subdirectory
      --skip-license    accept license

# run the installer
bash sortmerna-4.3.6-Linux.sh --skip-license
  sortmerna Installer Version: 4.3.6, Copyright (c) Clarity Genomics
  This is a self-extracting archive.
  The archive will be extracted to: $HOME/sortmerna
  
  Using target directory: /home/biocodz/sortmerna
  Extracting, please wait...
  
  Unpacking finished successfully

# check the installed binaries
ls -lrt /home/biocodz/sortmerna/bin/
sortmerna

# set PATH
export PATH=$HOME/sortmerna/bin:$PATH

# test the installation
sortmerna --version
  SortMeRNA version 4.3.6
  Build Date: Jul 17 2021
  sortmerna_build_git_sha:@921fa40256760ea2d44c49b21eb326afda748d5e@
  sortmerna_build_git_date:@2022/08/16 10:59:31@

# view help
sortmerna -h

Running

  • The only required options are --ref and --reads
  • Options (any) can be specified usig a single dash e.g. -ref and -reads
  • Both plain fasta/fastq and archived fasta.gz/fastq.gz files are accepted
  • file extensions .fastq, .fastq.gz, .fq, .fq.gz, .fasta, ... are optional. The format and compression are automatically recognized
  • Relative paths are accepted

for example

# single reference and single reads file
sortmerna --ref REF_PATH --reads READS_PATH

# for multiple references use multiple '--ref'
sortmerna --ref REF_PATH_1 --ref REF_PATH_2 --ref REF_PATH_3 --reads READS_PATH

# for paired reads use '--reads' twice
sortmerna --ref REF_PATH_1 --ref REF_PATH_2 --ref REF_PATH_3 --reads READS_PATH_1 --reads READS_PATH_2

More examples can be found in test.jinja and run.py

Refer to the Manual for usage details

Execution trace

Here is a sample execution trace.

IMPORTANT

  • Progressing exe