% 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

brew install brewsci/bio/dehomopolymerate

brew install -c bioconda dehomopolymerate

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

% 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)

% dehomopolymerate -v
dehomopolymerate 0.3

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

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

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