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@guilhermesena1 guilhermesena1 released this 20 Jan 20:45
· 260 commits to master since this release
v2.0.0
04f5510

The correct files to download are either abismal-2.0.0.zip or abismal-2.0.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This version of abismal has several improvements over abismal-1.0.0 (described below). Please note that any index built with 1.0.0 must be rebuilt, as they are not compatible with the current release.

List of changes:

  • The new index uses less memory. For hg38, the memory footprint for mapping is reduced from 3.5 GB to 2.7 GB
  • Abismal 2.0.0 now performs full alignments
  • Abismal 2.0.0 has algorithmic guarantees on exact matches. If a read matches the reference genome exactly somewhere, the match is guaranteed to be found.
  • Abismal 2.0.0 is faster in smaller genomes. Search parameters used internally are based on genome k-mer frequencies rather than "hard-coded", which improves speed in genomes like arabidopsis, chicken and bacteria.
  • A documentation is now available describing the SAM output format, a detailed description of each parameter and several examples of use.

Some issues are also resolved relative to the previous version:

  • 9c93354 : resolves an issue where abismal crashes if a long read is passed to it. If a read is larger than 65535, abismal will report an error message
  • the percent_unmapped report now shows 100 minus the percent_mapped (whereas before it showed 100 - percent_unique)
  • the error_rate is no longer a percentage, but rather a fraction
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