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0.4.0
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@paoloczi paoloczi released this 10 Jan 17:18
· 1997 commits to master since this release
0.4.0
e1cf3c7

Changes from release 0.3.0:

  • Shasta can now read uncompressed Fastq files directly without the need to convert to Fasta first. Each read in a Fastq file must be on exactly 4 lines.

  • Restrictions on reading Fasta files have been removed. Input reads can now be on multiple lines. Reads containing no-calls are discarded.

  • GPU acceleration.

  • Sample configuration files for various kinds for Oxford Nanopore and Pacific Biosciences reads at coverage around 60x. These reflect best known parameter choices as of December 2019. Default values of command line options remain mostly compatible with previous releases and are no longer recommended for any specific application.

  • New built-in Bayesian model for nanopore reads generated by the Guppy 3.0.5 base caller. Invoked via --Assembly.consensusCaller Bayesian:guppy-3.0.5-a. The default remains --Assembly.consensusCaller Bayesian:guppy-2.3.5-a.

  • New command line option --MinHash.minBucketSize provides more control of the MinHash/LowHash step. New output file LowHashBucketHistogram.csv can be used to select optimal values of --MinHash.minBucketSize and --MinHash.maxBucketSize.

  • Command line option --MinHash.minHashIterationCount can now be set to zero to adaptively select the number of MinHash iterations. Iteration stops when a specified number of alignment candidates per read
    (controlled by a new option --MinHash.alignmentCandidatesPerRead) is reached.

  • New command line option --Align.sameChannelReadAlignment.suppressDeltaThreshold can be used to suppress alignments between reads originating close in time from the same nanopore channel. This helps eliminate some assembly artifacts caused by some types of pathological reads.

  • New command line option --Align.maxDrift provides more control over the selection of marker alignments.

  • More options to select the k-mers to be used as markers (--Kmers.suppressHighFrequencyMarkers, --Kmers.enrichmentThreshold, --Kmers.file).

  • More flexible build system allows building Shasta as static or dynamic executable, static library (callable from C++), shared library (callable from C++ and Python), or AppImage. The static executable and the AppImage require no installation and run on a variety of Linux platforms.

  • Many usability and documentation improvements.

This release is not compatible with previous releases. There were incompatible changes in some command line option names, the binary formats used, and the Python API. You cannot use release 0.4.0 for postprocessing of an assembly done using a previous release.

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