biostars85929.pl - convert fastq to fasta

biostars85929.pl

#!/usr/bin/env perl

use strict;
use warnings;
use Bio::Factory::EMBOSS;

my $usage   = "perl $0 in.fq out.fa";
my $infile  = shift or die $usage;
my $outfile = shift or die $usage;

my $factory = Bio::Factory::EMBOSS->new;
my $seqret  = $factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication object

$seqret->run({-sequence => $infile,
              -sformat1 => 'fastq',
              -outseq   => $outfile,
              -osformat => 'fasta'});