SeqKit v2.0.0

Changelogs

• SeqKit v2.0.0 - 2021-08-27
  • Performance improvements
    • seqkit:
      • faster FASTA/Q reading and writing, especially on FASTQ, see the benchmark.
        • reading (plain text): 4X faster. seqkit stats dataset_C.fq
        • reading (gzip files): 45% faster. seqkit stats dataset_C.fq.gz
        • reading + writing (plain text): 3.5X faster. seqkit grep -p . -v dataset_C.fq -o t
        • reading + writing (gzip files): 2.2X faster. seqkit grep -p . -v dataset_C.fq.gz -o t.gz
      • change default value of -j/--threads from 2 to 4, which is faster for writting gzip files.
    • seqkit seq:
      • fix writing speed, which was slowed down in v0.12.1.
  • Breaking changes
    • seqkit grep/rmdup/common:
      • consider reverse complement sequence by default for comparing by sequence, add flag -P/--only-positive-strand. #215
    • seqkit rename:
      • rename ID only, do not append original header to new ID. #236
    • seqkit fx2tab:
      • for -s/--seq-hash: outputing MD5 instead of hash value (integers) of xxhash. #219
  • Bugfixes
    • seqkit seq:
      • fix failing to output gzipped format for file name with extension of .gz since v0.12.1.
    • seqkit tab2fx:
      • fix bug for very long sequences. #214
    • seqkit fish:
      • fix range check. #213
    • seqkit grep:
      • it's not exactly a bug: forgot to use multi-threads for -m > 0.
  • New features/enhancements
    • seqkit grep:
      • allow empty pattern files.
    • seqkit faidx:
      • support region with begin > end, i.e., returning reverse complement sequence
      • add new flag -l/--region-file: file containing a list of regions.
    • seqkit fx2tab:
      • new flag -Q/--no-qual for disabling outputing quality even for FASTQ file. #221
    • seqkit amplicon:
      • new flag -u/--save-unmatched for saving records that do not match any primer.
    • seqkit sort:
      • new flag -b/--by-bases for sorting by non-gap bases, for multiple sequence alignment files.#216