SeqKit v0.9.1

Changelog

• SeqKit v0.9.1
  
  • seqkit faidx: fix bug of retrieving subsequence with multiple regions on same sequence. #48
  • seqkit sort/shuffle/split: fix bug when using -2/--two-pass to process .gz files. #52

SeqKit v0.9.0

Changelog

• SeqKit v0.9.0
  • seqkit: better handle of empty file, no error message shown. #36
  • new subcommand seqkit split2: split sequences into files by size/parts (FASTA, PE/SE FASTQ). #35
  • new subcommand seqkit translate: translate DNA/RNA to protein sequence. #28
  • seqkit sort: fix bug when using -2 -i, and add support for sorting in natural order. #39
  • seqkit grep and seqkit locate: add experimental support of mismatch when searching subsequences. #14
  • seqkit stats: add stats of Q20 and Q30 for FASTQ. #45

SeqKit v0.8.1

Changlog

SeqKit v0.8.1

• seqkit: do not call pigz or gzip for decompressing gzipped file any more. But you can still utilize pigz or gzip by pigz -d -c seqs.fq.gz | seqkit xxx.
• seqkit subseq: fix bug of missing quality when using --gtf or --bed
• seqkit stats: parallelize counting files, it's much faster for lots of small files, especially for files on SSD

SeqKit v0.8.0

Changelog

SeqKit v0.8.0

• seqkit, stricter FASTA/Q format requirement, i.e., must starting with > or @.
• seqkit, fix output format for FASTQ files containing zero-length records, yes this happens.
• seqkit, add amino acid code O (pyrrolysine) and U (selenocysteine).
• seqkit replace, add flag --nr-width to fill leading 0s for {nr}, useful for preparing sequence submission (">strain_00001 XX", ">strain_00002 XX").
• seqkit subseq, require BED file to be tab-delimited.

SeqKit v0.7.2

Changelog

SeqKit v0.7.2

• seqkit tab2fx: fix a concurrency bug that occurs in low proprobability when only 1-column data provided.
• seqkit stats: add quartiles of sequence length
• seqkit faidx: add support for retrieving subsequence using seq ID and region, which is similar with "samtools faidx" but has some extra features

SeqKit v0.7.1

Changelog

SeqKit v0.7.1

• seqkit convert: fix bug of read quality containing only 3 or less values. shenwei356/bio/issues/3
• seqkit stats: add option -T/--tabular to output in machine-friendly tabular format. #23
• seqkit common: increase speed and decrease memory occupation, and add some notes.
• fix some typos. #22
• suggestion: please install pigz to gain better parsing performance for gzipped data.

SeqKit v0.7.0

Changelog

• add new command convert for coverting FASTQ quality encoding between Sanger, Solexa and Illumina. Thanks suggestion from @cviner ( #18). usage & example.
• add new command range for printing FASTA/Q records in a range (start:end). #19. usage & example.
• add new command concate for concatenating sequences with same ID from multiple files. usage & example.

SeqKit v0.6.0 with bash-completion support

Changelog

• add new command genautocomplete to generate shell autocompletion script! (#17)
• add new command seqkit dup for duplicating sequences (#16)
• seqkit stats -a does not show L50 which may brings confusion (#15)
• seqkit subseq --bed: more robust for bad BED files

SeqKit v0.5.5

Changelog

• Increasing speed of reading .gz file by utilizing gzip (1.3X),
  it would be much faster if you installed pigz (2X).
• Fixing colorful output in Windows
• seqkit locate: add flag --gtf and --bed to output GTF/BED6 format,
  so the result can be used in seqkit subseq.
• seqkit subseq: fix bug of --bed, add checking coordinate.

SeqKit v0.5.4

Changelog

• seqkit subseq --gtf, add flag --gtf-tag to set tag that's outputted as sequence comment
• fix seqkit split and seqkit sample: forget not to wrap sequence and quality in output for FASTQ format
• compile with go1.8.1