ABySS pipeline

ABySS specifications


Unique identifier OMICS_00006
Name ABySS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Perl, Shell (Bash)
Parallelization MPI
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.2
Stability Stable
Source code URL https://codeload.github.com/bcgsc/abyss/tar.gz/2.0.2
Maintained Yes
Wikipedia https://github.com/bcgsc/abyss/wiki



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  • person_outline Inanc Birol <>
  • person_outline Anthony Raymond <>

Additional information


Publications for ABySS

ABySS citations

PMCID: 5843731

[…] average read length). the quality of the illumina reads was improved by trimming off low-quality bases using bbduk (bbmap suite version 36.77). high-quality reads were assembled into contigs using abyss version 2.0.2 (4). the long reads were mapped to the draft assembly using basic local alignment with successive refinement (blasr) (5). based on these alignments, the contigs were linked […]

PMCID: 5721137

[…] the whole genome was sequenced from paired-end libraries (truseq dna sample preparation kit, illumina, san diego, ca, usa) using 10% of an illumina hiseq 2500 lane. reads were assembled using abyss-pe v1.2.7 utilizing the reads with kmer set to 90 bases. remaining gaps were closed using conventional pcr followed by sanger sequencing giving a contiguous sequence of 2,994,740 bases. […]

PMCID: 5738614

[…] sequence reads were filtered against 42 myrtaceae cp genomes (table s1) using bwa software with two mismatches allowed (li and durbin, 2009). the obtained reads were assembled de novo with abyss software (simpson et al., 2009). the cp genome scaffolds were orientated using cp genome sequences of eucalyptus globulus, eucalyptus grandis and eugenia uniflora l. using blastn (camacho et […]

PMCID: 5929187

[…] on a hiseq 1500 using the 2 × 50 paired-end protocol. reads in fastq format were quality-filtered, and any adapter sequences were removed, using trimmomatic software.18 the de novo assembly program abyss19 was used to assemble the reads into contigs, using several different sets of reads, and k values from 20 to 40. in all samples, host reads were filtered out before de novo assembly. […]

PMCID: 5519584

[…] m. glaziovii (samn02693380)., sequence quality assessment was done using fastqc (patel and jain, 2012). the first 10 bases were trimmed using fastx trimmer and then de novo assembly performed using abyss-pe (simpson et al., 2009). default parameters were used with a k-mer of 64. the purpose of assembling the kiroba genome was to obtain high quality scaffolds for alignment and snp analysis. […]

ABySS institution(s)
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
ABySS funding source(s)
Supported by the National Human Genome Research Institute of the National Institutes of Health (under award no. R01HG007182), with additional support provided by Intel, Genome Canada, Genome British Columbia, and the British Columbia Cancer Foundation.

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