Corset protocols

Corset specifications

Information


Unique identifier OMICS_12944
Name Corset
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 1.07
Stability Stable
Requirements SAMtools
Maintained Yes

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Documentation


Maintainer


  • person_outline Alicia Oshlack <>

Additional information


https://github.com/Oshlack/Corset/wiki

Publication for Corset

Corset IN pipelines

 (5)
2017
PMCID: 5469171
PMID: 28616064
DOI: 10.1111/eva.12463

[…] retained 93%–95% of read pairs (table s1). of these, a large proportion of high‐quality read pairs (91%–94%) were mapped to the respective species de novo transcript reference (table s1). corset transcript clustering reduced the number of unique “genes,” or transcript clusters, to 63,231 for round goby and 57,468 for tubenose goby, and of these, 26,215 genes for round goby and 23,648 […]

2017
PMCID: 5695279
PMID: 29125846
DOI: 10.1371/journal.pone.0187738

[…] 219,831 transcripts with average length of 771 bp and n50 of 1302 bp (table 2). the length distribution of transcripts is showing in s1 fig. the de novo assembled transcriptomes were clustered by ‘corset’, which is a method and software for obtaining gene-level counts from any de novo transcriptome assembly [32]. after clustering by corset, a total of 139,863 clusters were obtained, […]

2017
PMCID: 5695279
PMID: 29125846
DOI: 10.1371/journal.pone.0187738

[…] fig. the de novo assembled transcriptomes were clustered by ‘corset’, which is a method and software for obtaining gene-level counts from any de novo transcriptome assembly [32]. after clustering by corset, a total of 139,863 clusters were obtained, in which the clusters with longest sequences were defined as unigenes. finally a total of 139,333 unigenes with average length of 1049 bp and n50 […]

2017
PMCID: 5827264
PMID: 29183907
DOI: 10.1242/bio.028498

[…] can be used to create consensus gene sequences. however, since both programs perform their clustering based on all transcript sequences, paralogous genes may be erroneously merged. in contrast, corset (davidson and oshlack, 2014) identifies sequence similarity between transcripts by identifying multi-mapped reads resulting from re-mapping of reads against the reconstructed transcriptome. […]

2016
PMCID: 4893630
PMID: 27264734
DOI: 10.1038/srep27357

[…] of botryllus genome, which in the current assembly state is not satisfactory. for this reason the other two methodologies based on de novo transcriptomes were adopted. as methodology 3 (applying corset clustering algorithm) showed a higher mapping percentage (supplementary table s3), so at first it appeared as a better approach to further analyze the sequencing data. though on one hand, […]

Corset institution(s)
Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia; Department of Genetics, University of Melbourne, Melbourne, VIC, Australia
Corset funding source(s)
Supported by an NHMRC Career Development Fellowship APP1051481.

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