dehomopolymerate

Collapse sequence homopolymers to a single character

Quick Start

% cat test/test.fq

@SRR2288572.2 /1
GAATTTCCCC
+
"!!"!"!!!!
@SRR2288572.2 /1
TCGTGTTTTCTTTTTCTTTT
+
"!!"!"!!!!!!!!!!!!!!

% dehomopolymerate test/test.fq

@SRR2288572.2
GATC
+
"!"!
@SRR2288572.2
TCGTGTCTCT
+
"!!"!"!!!!

INPUT  : seqs=2 bp=30 avglen=15
OUTPUT : seqs=2 bp=14 avglen=7

Installation

Homebrew

brew install brewsci/bio/dehomopolymerate

Conda

brew install -c bioconda dehomopolymerate

From source

dehomopolymerate is written in C to the C99 standard and only depends on gcc and libz.

git clone https://github.com/tseemann/dehomopolymerate.git
cd dehomopolymerate
make 
make install PREFIX=$HOME/bin

Options

-h (help)

% dehomopolymerate -h

SYNOPSIS
  Collapse sequence homopolymers to a single character
USAGE
  dehomopolymerate [options] reads.fast{aq}[.gz] > nohomop.fq
OPTIONS
  -h      Show this help
  -v      Print version and exit
  -q      Quiet mode; not non-error output
  -f      Output FASTA not FASTQ
  -w      Output RAW one line per sequence
  -l LEN  Discard output sequences shorter then L bp
URL
  https://github.com/tseemann/dehomopolymerate (Torsten Seemann)

-v (version)

Prints the name and version separated by a space in standard Unix fashion.

% dehomopolymerate -v
dehomopolymerate 0.3

-q (quiet)

Don't print informational messages, only errors.

-f (FASTA output)

% dehomopolymerate -f test/test.fq.gz
>SRR2288572.2
GATC
>SRR2288572.2
TCGTGTCTCT

-w (raw sequence output, one per line)

% dehomopolymerate -w test/test.fq.gz
GATC
TCGTGTCTCT

-l MINLEN (minimum length of output sequences)

% dehomopolymerate -l 6 -f test/test.fq.gz
>SRR2288572.2
TCGTGTCTCT

Issues

File concerns at the Issue Tracker

License

GPLv3

Author

• Torsten Seemann