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Title: v0.3.0

Type Software Richard Smith-Unna, cboursnell (2014): v0.3.0. Zenodo. Software. https://zenodo.org/record/11037

Authors: Richard Smith-Unna (University of Cambridge) ; cboursnell ;

Links

Summary

Features:

metrics on each contig are now calculated and output to a file (by default, transrate_contigs.csv) output files can have a custom prefix with the --outfile argument

Improvements:

all inline C methods replaced with extension C (cleaner code, only compiles once on install) linguistic complexity now calculated in C (400x speedup) support new CRB-BLAST feature that splits BLAST query into one chunk per core (faster than threaded BLAST in most cases) check dependencies at every run and give instructions for installing them if missing

Bug fixes:

remove redundant express dependency fix parsing of samtools mpileup output so contig names are now matched up fix bug where null characters in contigs weren't handled (wtf are null characters doing in contigs, Trinity?) handle all bases that aren't ACTG by considering them to be Ns

More information

  • DOI: 10.5281/zenodo.11037

Dates

  • Publication date: 2014
  • Issued: July 25, 2014

Rights

  • info:eu-repo/semantics/openAccess Open Access

Much of the data past this point we don't have good examples of yet. Please share in #rdi slack if you have good examples for anything that appears below. Thanks!

Format

electronic resource

Relateditems

DescriptionItem typeRelationshipUri
IsSupplementTohttps://github.com/Blahah/transrate/tree/v0.3.0
IsVersionOfhttps://doi.org/10.5281/zenodo.591478
IsPartOfhttps://zenodo.org/communities/zenodo