abyss

About

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

Versions and Availability

Module Names for abyss on smic
Machine Version Module Name
smic 1.5.2 abyss/1.5.2/INTEL-140-MVAPICH2-2.0
smic 1.9.0 abyss/1.9.0/INTEL-140-MVAPICH2-2.0
▶ **FIX-ME** FAQ?

Usage

A set of various tools are included in this suite: 
ABYSS 
abyss-bwamem 
abyss-gapfill 
abyss-map 
abyss-scaffold 
abyss-align 
abyss-bwasw 
abyss-gc 
abyss-map-ssq 
abyss-tabtomd

To find out how to use these tools, type "tool --help"

For example: ABYSS --help
Usage: ABYSS -k -o [OPTION]... FILE...
e.g., ABYSS -k20 reads.fastq.gz -o configs.fa
	

Resources

Last modified: June 18 2015 17:03:55.