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Arioc v1.51

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@RWilton RWilton released this 23 Sep 00:18
· 12 commits to master since this release
v1.51
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Notes for Arioc v1.51:

The current build is v1.51.3140 (17 May 2023).

This is a stable, performance-tested build.

Arioc v1.51 reference-genome lookup tables are incompatible with those generated by AriocE in release v1.43 and earlier. If you are upgrading to v1.51 from an earlier version of Arioc, please re-execute AriocE to create new lookup tables. Updated lookup tables for the human, mouse, and bread yeast reference genomes are available at ftp://ftp.ccb.jhu.edu/pub/data/Arioc, the FTP server for the Center for Computational Biology at Johns Hopkins University.

New features

  • AriocU, AriocP: increased accuracy of MAPQ computation model
  • AriocU, AriocP: configuration parameter AtN is no longer supported
  • AriocU, AriocP: binary output formats specific for the Terabase Search Engine (TSE, KMH) are no longer supported
  • AriocU, AriocP: in repetitive regions where the placement of a short variant (SNV, indel) is arbitrary (upper track in the following image), Arioc reports the "leftmost" location within the region (lower track in the following image); this behavior is consistent with BWA and Bowtie 2 and may facilitate variant identification in repetitive regions with low coverage:
     
    chr14:26763381
  • AriocP: increased depth-of-search in gapped alignment of mates whose opposite mate has a reportable nongapped mapping
  • AriocU, AriocP: in seed-and-extend gapped alignment, added a seed-prioritization heuristic that prioritizes higher-scoring mappings for the first seeds examined; this decreases (although it does not entirely eliminate) cases where a lower-scoring but reportable mapping precludes the identification of a higher-scoring mapping associated with the last seeds examined for a read sequence.
  • AriocU, AriocP: added the subRate ("substitution rate") for tuning MAPQ performance; this replaces the errorRate parameter implemented in previous Arioc versions.
  • AriocU, AriocP: added the xmBQS parameter to specify a base quality score threshold for reporting methylation context for bisulfite-treated read sequences.
  • AriocU, AriocP: maxJ is now a required configuration parameter.

Bug fixes

  • AriocE: corrupted defline in reference sequence longer than 21 million bases in FASTA file containing multiple reference sequences (see #31).
  • AriocP: incorrect alignment score (AS) reported for occasional mates aligned by Smith Waterman alignment within regions "anchored" by their mapped opposite mates.
  • AriocU, AriocP: data-dependent CUDA memory access exception when lookup tables are partitioned across four or more GPU devices (useHJinGPmem="1").
  • AriocE: possible error in multithreaded generation of genome configuration metadata.

Downloads

file content
Arioc.RQA.151.zip Linux examples
Arioc.w.151.zip Windows source code
Arioc.x.151.zip Linux source code
AriocSetup.msi Windows binaries and examples
Assets 6