ABYSS - assemble short reads into contigs




Assemble all input files, FILE, which may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and may be compressed with gz, bz2 or xz and may be tarred.

Users wishing to run a full assembly with ABySS are recommended to use abyss-pe as their entry point rather than the ABYSS program. abyss-pe is a Makefile that coordinates many of the ABySS tools (including ABYSS) in order to run the full ABySS assembly pipeline. abyss-pe is capable of doing many things that ABYSS is not, such as leveraging the distance information provided by paired end reads and mate pair reads.

discard unchaste reads [default]
do not discard unchaste reads
trim masked bases from the ends of reads [default]
do not trim masked bases from the ends of reads
-q, --trim-quality=THRESHOLD
trim bases from the ends of reads whose quality is less than the threshold
zero quality is `!' (33)
default for FASTQ and SAM files
zero quality is `@' (64)
default for qseq and export files
-o, --out=FILE
write the contigs to FILE
-k, --kmer=KMER_SIZE
k-mer size
-t, --trim-length=TRIM_LENGTH
maximum length of dangling edges to trim
-c, --coverage=COVERAGE
remove contigs with mean k-mer coverage less than this threshold
-b, --bubbles=N
pop bubbles shorter than N bp (default: 3*k).
-b0, --no-bubbles
do not pop bubbles
-e, --erode=COVERAGE
erode bases at the ends of blunt contigs with coverage less than this threshold
-E, --erode-strand=COVERAGE
erode bases at the ends of blunt contigs with coverage less than this threshold on either strand
record the k-mer coverage histogram in FILE
-g, --graph=FILE
generate a graph in dot format
-s, --snp=FILE
record popped bubbles in FILE
-v, --verbose
display verbose output
display this help and exit
output version information and exit


Written by Jared Simpson and Shaun Jackman.


Report bugs to <>.


Copyright 2013 Canada's Michael Smith Genome Science Centre

Latest Tech News
Your Notes

Sign in/Sign up

Signing in to our system allows you to post your contributions and vote on the contributions of others. It will also allow you to get extra perts like having your favorites in the cloud and having your persistent personal notes wherever you go. More will be added as we scale up our services.

By signing in to our system, you agree our Member Terms and Conditions

with one of the following services

Almost finished!

Please select a screen name for NET SOUP.

 Please send me news and special offers from NET SOUP.

 I have read and accept the Terms of Use.


We have no example yet for this entry

Your Name

Community Contributions and Discussions

Modify your search

View Documentation

Jobs from Indeed