SSPACE

Introduction

Software from Baseclear for improving N50 on de-novo assemblies.

Usage

To load it up

module load SSPACE

SSPACE needs a configuration file before being run, speified b the -l option. This file specifies what the input to the program should be. Here is an example:

lib1 bowtie SRR001665_1.fastq.gz SRR001665_2.fastq.gz 200 0.25 FR

There is one line per pair of short read files. However it does not mention the contigs file one is seeking to improve. This is given in the command line options with the -s option. Here is an example command line:

SSPACE.pl -l libraries.txt -s contigs_abyss.fasta -k 5 -a 0.7 -x 0 -b ecoli_scafs_next