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  • Improve the efficiency for computing average genome size (could this resolve the abundance 0 issue?)
  • Fixing an issue when building the index for very short sequences
  • Fixing an issue when using "host-genome"
  • Update documentation
  • Fix several compilation issues
  • Improve the support of lowest common ancestor (lca) in centrifuge-promote and centrifuge-kreport
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  • Support running multiple samples while loading index only once. (#95 .Thanks to Daniel Maple @maplesond)
  • Fix a bug of misassignment if a read comes near the boundary of a genome. (#97 )
  • centrifuge-kreport uses the lowest common ancestor taxonomy id for multiple assigned reads by default.
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  • Fix several bugs.
  • Output unclassified reads.
  • Make the options about output the sequences (--un,--al,--un-conc,--al-conc) work.
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Centrifuge 1.0.3-beta release 12/06/2016

  • Fixed Perl hash bangs (thanks to Andreas Sjödin / @druvus).
  • Updated nt database building to work with new accession code scheme.
  • Added option --tab-fmt-cols to specify output format columns.
  • A minor fix for traversing the hitmap up the taxonomy tree.
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  • Fixed a runtime error during abundance analysis.
  • Changed a default report file name from centrifuge_report.csv to centrifuge_report.tsv.

Genome Research version of Centrifuge

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  • Centrifuge is now able to work directly with SRA data: both downloaded on demand over internet and prefetched to local disks.
  • For example, you can run Centrifuge with SRA data (SRR353653) as follows.
    centrifuge -x /path/to/index --sra-acc SRR353653
  • This eliminates the need to download SRA reads manually and to convert them into fasta/fastq format without affecting the run time.
  • We provide a Centrifuge index (nt index) for NCBI nucleotide non-redundant sequences collected from plasmids, organelles, viruses, archaea, bacteria, and eukaryotes, totaling ~109 billion bps. Centrifuge is a very good alternative to Megablast (or Blast) for searching through this huge database.
  • Fixed Centrifuge's scripts related to sequence downloading and index building.