Centrifuge v1.0.4.1

• Improve the robustness of centrifuge-download (#201 ). There are still some download issues that need to be addressed in future versions, e.g. #262, #263.
• Properly handle the "--temp-directory" option. (#268)
• Fix several documentation errors.

Centrifuge v1.0.4

• 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

Centrifuge v1.0.4-beta

• 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.

Centrifuge v1.0.3

• Fix several bugs.
• Output unclassified reads.
• Make the options about output the sequences (--un,--al,--un-conc,--al-conc) work.

v1.0.3-beta

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.

v1.0.2-beta

• 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

Genome Research version of Centrifuge

Centrifuge 1.0.1-beta release 3/8/2016

• 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.