fill_gaps_with_gapfiller - Given an assembly iteratively fill gaps
version 1.160490
Given an assembly and some reads in fastq format, try and fill in the gaps. Do multiple iterations with different values, and cleanup all intermediate files.
# outputs a file called contigs.scaffolded.fa fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq # use two threads (default 1) fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2 # Gzipped input files are accepted fill_gaps_with_gapfiller -a contigs.fa.gz -f 123_1.fastq.gz -r 123_2.fastq.gz # Insert size defaults to 250 if not specified fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -i 3000 # This help message fill_gaps_with_gapfiller -h
Andrew J. Page <ap13@sanger.ac.uk>
This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
To install Bio::AssemblyImprovement, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::AssemblyImprovement
CPAN shell
perl -MCPAN -e shell install Bio::AssemblyImprovement
For more information on module installation, please visit the detailed CPAN module installation guide.