Bioinformatics at COMAV


The recommended method to get seq_crumbs is to download one of the releases, but if you want to access to the latest code you can do it at github.

seq_crumbs 0.1.9


  • Remove third party binaries. (blast, bwa, bowtie2, samtools)
  • Pair_matcher now works with orphans
  • Filter sequences composed only by Ns implemented(filter_all_ns)
  • classify_chimeras binary added
  • draw_pair_distance_distribution binary added
  • trim_mp_chimeras binary added
  • filter by blast short implemented
  • Tons of bugfixes

Released on 24-11-2014

seq_crumbs 0.1.8


  • trim binaries now handle paired seqs
  • added write xml_traceinfo file option to sff_extract
  • count seqs binary added
  • biopython is now optional
  • several bugfixes

Released on 21-5-13

seq_crumbs 0.1.7


  • Performance gains in pair related binaries and cat_seqs, sample_seqs and seq_heads
  • Output format will be the same as input format, except for convert_format
  • new binary: fastqual_to_fastq
  • several bugfixes

Released on 10-2-13

seq_crumbs 0.1.6


  • Bugfix: Not all mate pairs were splitted. (thanks to Giuseppe)

Released on 10-12-12

seq_crumbs 0.1.5


  • orientate_transcripts executable added
  • dust complexity filtering implemented in filter_by_complexity
  • dust complexity scores distribution in calculate_stats
  • N50 is included in the calculate_stats report
  • seq_crumbs settings can now be set using environment variables
  • blast+ updated to 2.2.27
  • Several bug fixes done.

Released on 26-11-12

seq_crumbs 0.1.4


  • filter_by_length accepts maximum and minimum length thresholds
  • ascii bloxplot now fits in smaller terminals

Released on 7-11-12

seq_crumbs 0.1.3


  • sff_extract advice fixed

Released on 22-10-12

seq_crumbs 0.1.2


  • added kmer freq stats to calculate stats
  • sff_extract now recommends how many nucleotides to trim
  • several bugfixes

Released on 22-10-12

seq_crumbs 0.1.1


  • added filter_by_blast
  • several bugfixes

Released on 18-10-12

seq_crumbs 0.1

Released on 04-10-12

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