ABySS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ABySS
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Tool usage distribution map

This map represents all the scientific publications referring to ABySS per scientific context
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Associated diseases

This word cloud represents ABySS usage per disease context
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Popular tool citations

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Protocols

ABySS specifications

Information


Unique identifier OMICS_00006
Name ABySS
Alternative name Assembly By Short Sequences
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

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Inanc Birol
  • person_outline Anthony Raymond

Additional information


https://github.com/bcgsc/abyss#abyss

Publications for Assembly By Short Sequences

ABySS citations

 (332)
library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] ible sequencing errors based on the distribution of Kmer frequencies using SOAPec v2.01 with default settings []. We then built de novo assemblies from the edited reads using SOAPdenovo2 v2.04 [] and ABySS v1.9.0 []. We also assembled the genome with MaSuRCA v2.3.2 [], which uses its own raw data quality control tools. For computational feasibility, the three assemblies used Kmer values of 63, 63, […]

library_books

Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

2018
PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] pair-ends. Raw reads were trimmed with an in house perl script to remove low quality reads (N > 10%, or sQ ≤ 5) and reads with adaptor contamination. Clean reads were then de novo assembled using the AbySS assembler version 1.3.5 [], with a Kmer value of 50. GapFiller version 2.0 [] was used to further fill gaps and generate scaffolds. The generated genome assembly was deposited at GenBank under a […]

library_books

A phylogenomic framework and timescale for comparative studies of tunicates

2018
BMC Biol
PMCID: 5899321
PMID: 29653534
DOI: 10.1186/s12915-018-0499-2

[…] jei (mix of several individuals) []. Previously obtained 454 transcriptomic data for Microcosmus squamiger [] were also considered. De novo assemblies were conducted with Trinity [] for 454 reads and ABySS [] for Illumina reads using the programs’ default parameters. For both kinds of libraries, we confirmed the sample taxonomic identifications by assembling the mitochondrial cytochrome c oxidase […]

library_books

Draft Genome Sequence of Janthinobacterium sp. Strain ROICE36, a Putative Secondary Metabolite Synthesizing Bacterium Isolated from Antarctic Snow

2018
Genome Announc
PMCID: 5897808
PMID: 29650588
DOI: 10.1128/genomeA.01553-17

[…] lity regions were filtered out with Trimmomatic software (), and the final data set contained 2,294,412 high-quality paired-end reads. De novo assembly was performed on the error-corrected reads with AbySS (), Velvet (), and SPAdes () bioinformatics tools; the SPAdes software produced the best assemblies, which were further evaluated with QUAST (). The final assembly contained 207 contigs, with a […]

library_books

Draft Genome Sequence of the Basidiomycete White Rot Fungus Phlebia centrifuga

2018
Genome Announc
PMCID: 5887033
PMID: 29622620
DOI: 10.1128/genomeA.01414-17

[…] version 2.05, a GenomeScan in-house pipeline, was used for adapter removal and quality checking; bases with a Phred score above Q22 and reads longer than 36 bp passed the filtering. For the assembly, ABySS version 1.3.7 (), with a k-mer length of 64, was used. Scaffolds shorter than 500 bp were removed. A total of 1,367 contigs were used for the assembly of the 34.66-Mb genome. The GC content was […]

library_books

Tracking the NGS revolution: managing life science research on shared high performance computing clusters

2018
GigaScience
PMCID: 5928410
PMID: 29659792
DOI: 10.1093/gigascience/giy028

[…] tatistical inference []) support task continuation on an ad hoc basis, but formal intermediate checkpoints are found in only a handful of multistage tools such as the genome assemblers MaSuRCA [] and ABySS [].Second, NGS software tools could provide the ability to limit the amount of RAM used. NGS tools that allow the user to specify memory limits are few in number; Java-based tools and the assemb […]


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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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