Trans-ABySS protocols

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Trans-ABySS specifications

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Unique identifier OMICS_01326
Name Trans-ABySS
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.5.5
Stability Stable
Requirements
ABySS, python-igraph, BLAT
Maintained Yes

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https://github.com/bcgsc/transabyss

Publication for Trans-ABySS

Trans-ABySS in pipelines

 (7)
2017
PMCID: 5279776
PMID: 28135292
DOI: 10.1371/journal.pone.0170914

[…] is kleat []. in contrast to other poly(a) read mapping approaches, it is based on de novo transcriptome assembly as a first step, using established transcriptome assembly approaches, such as trans-abyss []. in a second step, reads are re-aligned to the resulting contigs and contigs are aligned to the genome. from these alignments, three types of evidence are collected (tails, bridges, […]

2017
PMCID: 5279776
PMID: 28135292
DOI: 10.1371/journal.pone.0170914

[…] the minimum poly(a) read support rs appear to be most decisive., poly(a) site mapping using contextmap 2 with default parameters was compared against results obtained with kleat version 1.0 using trans-abyss for transcript assembly. transcript assembly was performed with k-mer lengths of 32, 52 and 72 and kleat poly(a) site predictions with at least 3 tail and bridge reads were evaluated. […]

2017
PMCID: 5279776
PMID: 28135292
DOI: 10.1371/journal.pone.0170914

[…] and kleat applied to the trans-abyss output. thus, total cpu time for poly(a) site prediction using contextmap 2 was less than a third of what was required by the full kleat workflow., runtime of trans-abyss using k-mer lengths of 32, 52 and 72, kleat applied to the trans-abyss output, and contextmap 2 using default parameters was obtained using 8 cores on the same machines and measured using […]

2016
PMCID: 4803216
PMID: 27003722
DOI: 10.1371/journal.pone.0152147

[…] while the redundancy in the p. excessana sequences was removed after the assembly using cd-hit []. de novo assembly of the processed reads was performed for each of the individual libraries () with trans-abyss (version 1.3.2) [], where a k-mer series of 31 to 75 with an increment of two bases was used for the libraries of p. octo, whereas k-mer values from 31 to 71 were used for the p. […]

2015
PMCID: 4446339
PMID: 26017144
DOI: 10.1371/journal.pone.0128596

[…] and trimmed by 15 bases from the 5' end and reads containing ns or mononucleotides were removed using in-house perl scripts. de novo assembly of the individual libraries was then performed by trans-abyss (version 1.3.2) [], where a k-mer series from k = 31 to k = 75 with an increment of two was used., blast searchable databases consisting of transcriptomic contigs from male and female e. […]


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Trans-ABySS in publications

 (91)
PMCID: 5940140
PMID: 29559535
DOI: 10.1534/g3.118.200257

[…] only needle tissue., variation in de novo transcriptome assembly is heavily influenced by the assembly software selected. the open source software packages for constructing transcriptomes includes: trans-abyss, velvet/oasis, soapdenovo, and trinity. it is unlikely that each of these would create assemblies of equal caliber. the assembly for western white pine used the commercial clc workbench […]

PMCID: 5793777
PMID: 29092957
DOI: 10.1101/mcs.a002329

[…] different ploidy at various tumor contents. tumor content and sequencing coverage for each case are provided in . structural variation was detected by de novo assembly of tumor reads using abyss and trans-abyss (), followed by variant discovery using delly (). rna-seq reads were processed and gene expression analyzed as previously described in ., in the absence of matched normal transcriptome […]

PMCID: 5825881
PMID: 29492338
DOI: 10.7717/peerj.4392

[…] and assembly procedures were described in and . ab initio gene and protein model predictions were obtained by using augustus trained with (i) de novo transcriptome assemblies obtained using trans-abyss for the corresponding species of phytophthora and dothideomycetes ( “rna-seq libraries”) or (ii) gene and protein sets from closely related species for the pucciniales. […]

PMCID: 5793095
PMID: 29271884
DOI: 10.3390/toxins10010008

[…] bp), but of lower quality [,]. the fragments can be assembled back into full length or partial transcripts (the assembled fragments being called contigs) using different software, such as trinity, trans-abyss or soapdenovo []., an older technology still in use today consists in using the classical sanger sequencing of expressed sequence tags (ests), which are short dna sequences obtained […]

PMCID: 5741667
PMID: 29273779
DOI: 10.1038/s41467-017-01964-9

[…] genomic libraries were assembled into contigs using abyss (28) using a k = 71. illumina paired-end rnaseq reads from representative body sections of p. waltl were assembled into transcripts using trans-abyss (29) (k = 69) with the aim to reconstruct only longer, complete transcripts rather than isoforms or short rnas. trans-abyss transcripts were then used to scaffold the genomic […]


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Trans-ABySS institution(s)
Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
Trans-ABySS funding source(s)
Supported, in part, by Genome Canada, Genome British Columbia, Michael Smith Foundation for Health Research and the Canadian Institute of Health Research (CIHR), including the CIHR Bioinformatics Training Program for Health Research.

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