ABySS protocols

ABySS specifications

Information


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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Documentation


Maintainers


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

Additional information


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

Publications for ABySS

ABySS IN pipelines

 (29)
2018
PMCID: 5764939
PMID: 29326215
DOI: 10.1128/genomeA.01430-17

[…] pipeline rta v1.18.64 and bcl2fastq v1.8.4. reads were trimmed for adapter sequences and filtered for sequence quality using the in-house tool fastqfilter v2.05. the short-read genome assembler abyss v1.3.7 (5) was used for assembly. an optimization for k-mer length was performed as in previous fungal genome assemblies. a length of 64 bp was found to give the best results, optimized […]

2017
PMCID: 5311727
PMID: 28201983
DOI: 10.1186/s12864-016-3480-x

[…] obtained by removing reads containing adapter, reads contains ploy-n (n > 10%), and low-quality reads (sq < = 5) from raw data. clean reads were then de novo assembled into scaffolds using the abyss assembler version 1.3.5 [24]. contigs representing mitochondrial genomic dnas were identified by blast search. gaps were filled by pcr and standard sanger sequencing, with the used primers […]

2017
PMCID: 5323629
PMID: 28232450
DOI: 10.1128/genomeA.01677-16

[…] and adaptor ligated, according to the illumina truseq dna preparation protocol, and condetri was implemented for trimming (16). cleaned and filtered nuclear reads were assembled de novo using abyss (17). all obtained sequences were aligned and manually reassembled., the hva980811 genome comprises 249,071 bp, including a 10,714-bp terminal direct repeat. the nucleotide sequence is 99% […]

2017
PMCID: 5331510
PMID: 28183770
DOI: 10.1128/genomeA.01607-16

[…] and adaptor ligated, according to the illumina truseq dna preparation protocol, and condetri was implemented for trimming (8). cleaned and filtered nuclear reads were assembled de novo using abyss (9). all obtained sequences were aligned and manually reassembled., the circular genomic dna comprised 16,930 bp and displayed very low similarity to known viruses, including jeecv. a blastn […]

2017
PMCID: 5356058
PMID: 28302781
DOI: 10.1128/genomeA.00043-17

[…] brazil, their guts were dissected, and the total dna was extracted and pooled. this dna was sequenced on an illumina miseq platform using a truseq library (8). the reads were de novo assembled using abyss v1.9 (9) with default parameters and a k-mer = 64. contigs larger than 800 nucleotides (nt) were analyzed by blastx against a local viral database. a contig of 8,030 nt corresponding […]

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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