Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Atropos trims reads with high sensitivity and specificity while maintaining leadingedge speed.

References:

• John P. Didion, Marcel Martin and Francis S. Collins
  Atropos: specific, sensitive, and speedy trimming of sequencing reads.
  PeerJ 5:e3720 https://doi.org/10.7717/peerj.3720

• Atropos Github page

• Module Name: atropos (see the modules page for more information)
• Implemented as a Singularity container
• Multithreaded
• Implements of a new insert alignment-based trimming algorithm for paired-end reads
• Options for trimming specific types of data (miRNA, bisulfite-seq)
• A new command ('detect') that will detect adapter sequences and other potential contaminants
• A new command ('error') that will estimate the sequencing error rate
• A new command ('qc') that generates read statistics similar to FastQC
• The ability to read SAM/BAM files and read/write interleaved FASTQ files
• Direct trimming of reads from an SRA accession
• Unusual environment variables set
  • ATROPOS_HOME  Atropos installation directory
  • ATROPOS_BIN       Atropos executable directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@@cn3316 ~]$ module load atropos

Create testing data in FASTA format:

[user@@cn3316 ~]$ printf ">myseq\\nACGTGCGCATGCCA" > test.fa
[user@@cn3316 ~]$ printf "printf "printf "@myseq\nACGTGCGCATGCCA\n+\n9C;=;=<9@4868>" > test.fastq

Run atropos on the sample data:

 atropos atropos -a CCA -se test.fa -o res.fa
...
=======
Atropos
=======

Atropos version: 1.1.18
Python version: 3.5.2
Command line parameters: trim -a CCA -se test.fa -o res.fa

Sample ID: test
Input format: FASTA, Read 1, w/o Qualities
Input files:
  /gpfs/gsfs7/users/denisovga/atropos/test.fa

Start time: 2018-05-10T21:59:41.572528
Wallclock time: 0.01 s (10000 us/read; 0.01 M reads/minute)
CPU time (main process): 0.01 s

--------
Trimming
--------

Reads                               records fraction
----------------------------------- ------- --------
Total reads processed:               1
Reads with adapters:                 1 100.0%
Reads written (passing filters):     1 100.0%

Base pairs                          bp fraction
----------------------------------- -- --------
Total bp processed:                 14
Total bp written (filtered):        11 78.6%

---------
Adapter 1
---------

Sequence Type       Length Trimmed (x)
-------- ---------- ------ -----------
CCA      regular 3'      3           1

No. of allowed errors:
0-3 bp: 0

Bases preceding removed adapters:
  A           0.0%
  C           0.0%
  G          100.0%
  T           0.0%
  none/other  0.0%

Overview of removed sequences:
length count expect max.err error counts
                            0           
------ ----- ------ ------- ------------
     3     1    0.0       0 1 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. atropos.sh). For example:

#!/bin/bash
module load atropos
# Create testing data in FASTQ format:
printf "printf "@myseq\nACGTGCGCATGCCA\n+\n9C;=;=<9@4868>" > test.fastq
atropos -a CCA -se test.fastaq -o res.fastaq

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] atropos.sh