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Plass Release 3-764a3
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@martin-steinegger martin-steinegger released this 05 Dec 21:23
· 126 commits to master since this release
3-764a3
764a3e7

Changes since Release 2-c7e35:

At a glance: Significant further development of the nucleotide assembler. Reduced hard disk requirements for protein assembler and many bug fixes.

Updated mmseqs submodule and adjusted plass to multiple MMseqs2 changes.

Breaking Changes

  • added reverse complement treatment for nucleotide sequences (plass nuclassemble)
  • introduced --kmer-per-seq-scale parameter to make sure not to miss good hits of long sequences. The number of extracted kmers can now be scaled with a user defined factor multiplied by the length of the sequence.
  • changed scoring mode for alignment calculation (--rescore-mode 3)

Features

  • add stdin support. cat reads.fas | plass assemble stdin asm tmp
  • reduced hard disk requirements by roughly a factor of 12 (--delete-tmp-inc)
  • added a first raw version of a cycle detector (still experimental) to avoid over extension for nucleotide assembly
  • introduced a new header format, which is now consistent for protein and nucleotide assembler
    <uniq ID> len:<len> cycle:<0|1> The cycle field is optional (for the nucleotide case)
  • introduced a new logic to handle sequences with N repeated k-mers: sequences with more than N repeated k-mers are no longer ignored in the assembly process completely, but instead repeated k-mers are only ignored in the kmermatcher phase. Replaced --skip-n-repeat parameter by --ignore-multi-kmer
  • overlaps are still sorted by ScorePerColumn but the bit score was replaced by the raw score to scale correctly with the overlap length
  • introduced --min-contig-len parameter to set minimum length of assembled contig to output (for nucleotide assembly)
  • added redundancy reduction (for nucleotide assembly) by clustering sequences based on user defined threshold (--clust-thr, default 0.97)
  • Dockerfile now uses Debian slim instead of alpine

Bugs

  • fixed problems in the first iteration of the protein assembler
  • fixed problems with start and stop codons occurring in the transition from protein alignments to nucleotide alignments and alignment offset calculation
  • split file existence check in workflows to individual checks to avoid repeated linking problems
  • fixed bug in the reverse complement calculation for N's in nucleotide sequences
  • fixed different problems for long sequences regarding the kmermatching phase
  • fixed broken compilation without zlib
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