ABySS protocols

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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

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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 in pipelines

 (84)
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 () 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 […]

2018
PMCID: 5773718
PMID: 29348333
DOI: 10.1128/genomeA.01418-17

[…] sequencing used the tagmentation procedure (). we generated a library of ~500 to 800 bp for subsequent sequencing on an illumina miseq instrument (2 × 300 nucleotides [nt]). after assembly using the abyss-pe program (), 24 contigs were assigned to the genome of c. taeniospiralis. these can be differentiated from the host genome by their nearly identical coverage and by their gc content of 41.5%, […]

2018
PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] rates of the short-insert pe library (shotgun dataset) using bwa vers. 0.7.5 with default parameters., based on the quality statistics we chose the assembly generated by combining ddn, besst, abyss and hirise (ddnbstabyhrs) to continue with the remainder of the analyses. we compared our assembly to genbank’s nt database using blastn (with evalue and output settings -evalue 0.0001 -outfmt […]

2018
PMCID: 5800051
PMID: 29402214
DOI: 10.1186/s12864-018-4490-7

[…] genome size of 2.46 ± 0.01 mb, see additional file : table s1). this de novo whole genome assembly (wga) of the f2 genome was conducted by processing a 90x short-reads dataset with a combination of abyss and sspace (see materials and methods). f2 genome size was estimated by k-mer frequency analysis to 2.47 gb, in agreement with flow cytometry estimation. this assembly represents 1597 mb (i.e., […]

2017
PMCID: 5289672
PMID: 28153886
DOI: 10.1128/genomeA.01508-16

[…] of paired-end 125 (pe125) via assembling and optimization according to paired-end and overlap relationships. the g+c content was calculated by gc-depth analysis. the reads were assembled de novo by abyss (), spades (), and mix (). based on the assembly results, the number of scaffolds is five, and the total coverage over the genome is 1,225-fold. the n50 value is 4,393,372 bp. the majority […]


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ABySS in publications

 (470)
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] 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, […]

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

[…] 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 […]

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

[…] (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 […]

PMCID: 5919021
PMID: 29652888
DOI: 10.1371/journal.pntd.0006410

[…] center biotechnology information (ncbi) under accession srp071001 of bioproject prjna312361 and biosample samn04497582., assembly of all reads was done as described previously using the assemblers abyss and soapdenovo-trans with every kmer ending in 1 and 5 (-k program switch) from 21 to 95 [–]. resulting contigs were re-assembled by a pipeline of blastn and cap3 assembler [] as described […]

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

[…] 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, […]


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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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