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@traymond traymond released this 01 May 23:58
· 1449 commits to master since this release
1.5.0
69fcedd

Summary

In this release we have added full strand specific RNA-Seq support such that output contigs are correctly oriented with respect to the original transcripts sequenced. Also, there are new parameters to abyss-pe, xtip and Q, that are used to improve assembly in high coverage regions like highly expressed transcripts. Setting xtip=1 will more aggressively remove certain tips. The Q parameter will prevent low quality bases from being used in the assembly. The version has been bumped to 1.5.0 to signify compatibility with Trans-ABySS 1.5.0.

ChangeLog

2014-01-15 Anthony Raymond [email protected]

  • Release version 1.5.0
  • Assemble strand-specific RNA-Seq libraries into strand-specific
    contigs.
  • New parameters, Q and xtip. Improves assembly in high-coverage
    regions by removing recurrent read errors.
  • Portability fixes for Fujitsu C Compiler.

abyss-pe:

  • New parameter, Q, to mask low quality bases to N.
  • New parameter, xtip=1, to remove 2-in 0-out tips.
  • New parameter, ss=1, to perform strand-specific assembly
    using ssRNA-Seq libraries.
  • New command, scaftigs. Breaks scaffold sequences at 'N's and
    produce a scaftigs.fa file.
  • Include long-scaffs.fa in FAC statistics if long parameter
    used.

abyss-fixmate:

  • Performance improvement for GCC-4.6 and older.

DistanceEst:

  • Report an estimation of duplicate fragments from read pairs
    mapping to different contigs.

abyss-fixmate:

  • Report number of fragments removed as noise and outliers.

ABYSS/ABYSS-P:

  • New option, --SS, to support strand-specific assembly.

abyss-layout:

  • New option, --SS, to support strand-specific assembly.

abyss-map:

  • New option, --SS, to support strand-specific assembly.

abyss-overlap:

  • New option, --SS, to support strand-specific assembly.

abyss-PathOverlap:

  • New option, --SS, to support strand-specific assembly.

abyss-scaffold:

  • New option, --SS, to support strand-specific assembly.
  • Don't prune xtips when scaffolding.

AdjList:

  • New option, --SS, to support strand-specific assembly.

Overlap:

  • New option, --SS, to support strand-specific assembly.

PopBubbles:

  • New option, --SS, to support strand-specific assembly.
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