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Releases
Existing and upcoming releases for this project.
Stable Releases
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ABySS 1.1.2
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Pop bubbles resulting from indels. Read tar files. Fix performance issues in ParseAligns by syncing KAligner threads periodically.
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ABySS 1.1.1
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Pop complex bubbles either completely or not at all. Choose better (typically lower) default values for the parameters e and c.
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ABySS 1.1.0
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ABySS will expand tandem repeats when it is possible to determine the exact number of the repeat. The paired-end path-finding algorithm, SimpleGraph, is multithreaded. Fixed a bug in MergePaths that could misassemble repeats larger than the paired-end fragment size. The output format of AdjList, DistanceEst and SimpleGraph has changed.
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ABySS 1.0.16
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Improve the performance and memory usage of KAligner and AdjList, particularly for very large data sets.
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ABySS 1.0.15
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New parameters, e and E, to set the coverage threshold of the erosion algorithm. Values for the parameters e and the coverage threshold, c, will be chosen automatically if they're not specified. The read length is now an optional parameter. Two important bug fixes, see below.
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ABySS 1.0.14
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Assemble multiple libraries of different fragment sizes.
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ABySS 1.0.13
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Read files compressed with gzip (.gz) or bzip2 (.bz2).
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ABySS 1.0.12
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Both ABYSS and KAligner are run only once per assembly, which speeds up the paired-end assembly stage by nearly a factor of two. The k-mer coverage information is correct in every contig file. A tool is included to convert colour-space contigs to nucleotide contigs. Discard reads that fail the chastity filter.
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ABySS 1.0.11
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Assemble colour-space reads. Read files in qseq format. KAligner is multithreaded. Integrate with Sun Grid Engine (SGE). Prevent misassemblies mediated by tandem segmental duplications.
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ABySS 1.0.10
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ParseAligns is improved to handle any number of reads as long as mate pairs are found interleaved in the same file. Merge overlapping paired-end contigs that were previously being missed in some situations. Number paired-end contigs so that their IDs do not overlap with the single-end contigs.
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ABySS 1.0.9
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Significantly reduce the memory usage of KAligner and ParseAligns. abyss-pe can read multiple input files and read FASTA or FASTQ files.
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ABySS 1.0.8
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Fix the bug causing the error Assertion `marked == split' failed.
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ABySS 1.0.7
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The parallel MPI assembler is now deterministic; it will produce the same result every time.
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ABySS 1.0.6
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Fix a race condition in the erosion algorithm.
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ABySS 1.0.5
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Portability fixes.
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ABySS 1.0.4
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Remove the need to specify the parameters -e,--erode and -b,--bubbles.
Use less disk space by using pipes to avoid intermediate files.
Many improvements to the paired-end algorithm.
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ABySS 1.0.3
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Tidy up the ends of blunt contigs. Merge blunt contigs that are connected by pairs and overlap.
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ABySS 1.0.2
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Include a parallel binary compiled for OpenMPI.
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ABySS 1.0
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Initial version of abyss.
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