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HISAT2-2.0.5 release 11/4/2016
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@infphilo infphilo released this 04 Nov 15:11
· 735 commits to master since this release
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Version 2.0.5 is a minor release with the following changes.

  • Due to a policy change (HTTP to HTTPS) in using SRA data (--sra-option), users are strongly encouraged to use this version. As of 11/9/2016, NCBI will begin a permanent redirect to HTTPS, which means the previous versions of HISAT2 no longer works with --sra-acc option soon.
  • Implemented -I and -X options for specifying minimum and maximum fragment lengths. The options are valid only when used with --no-spliced-alignment, which is used for the alignment of DNA-seq reads.
  • Fixed some cases where reads with SNPs on their 5' ends were not properly aligned.
  • Implemented --no-softclip option to disable soft-clipping.
  • Implemented --max-seeds to specify the maximum number of seeds that HISAT2 will try to extend to full-length alignments (see the manual for details).
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