ABySS 2.0.3 (Mar 14, 2018)


This minor release provides bug fixes and improved reliability for both MPI assemblies and Bloom filter assemblies on large datasets. In addition, many usability improvements have been made to the `abyss-samtobreak` program for misasssembly assessment.

For additional information about this project, please visit the overview page .

Available downloads

source code

For all platforms

Change log

2017-03-14 Ben Vandervalk <benv@bcgsc.ca>

* Many compiler fixes for GCC >= 6, Boost >= 1.64
* Read and write GFA 2 assembly graphs with `abyss-pe graph=gfa2`
* Support reading CRAM via samtools

* New `abyss-bloom build -t rolling-hash` option, to
pre-build input Bloom filters for `abyss-bloom-dbg`
* Fix incorrect output of `abyss-bloom kmers -r`
(thanks to @notestaff!)

* New `-i` option to read Bloom filter files built by
`abyss-bloom build -t rolling-hash`
* Improved error branch trimming (reduces number of
small output sequences)
* Fix intermittent segfaults caused by non-null-terminated

* Append BX tag to SAM output (Chromium 10x Genomics data)

* Increase default number of sparsehash buckets from
200,000,000 => 1,000,000,000
* Benefit: Allows larger datasets to be assembled without
time-consuming sparsehash resize operations (e.g. H. sapiens)
* Caveat: Increases minimum memory requirement per
CPU core from 89 MB to 358 MB

* Parallelize `gzip` with `pigz`, if available
* Report time/memory for each program with `zsh`, if available
* Fix: use `N` instead of `n` for scaffold stage,
when set by user

* New `--alignment-length` (`-a`) option to exclude alignments
shorter than a given length
* New `--contig-length` (`-l`) option to exclude contigs
shorter than a given length
* New `--genome-size` (`-G`) option, for contiguity metrics
that depend on the reference genome size
* New `--mapq` (`-q`) option for minimum MAPQ score
* New `--patch-gaps` (`-g`) option to join alignments
separated by small gaps
* New TSV output format with additional contiguity
stats (e.g. L50, NG50)
* Fix handling of hard-clipped alignments

* New `--add-complements` option

* New `--bx` option to copy BX tag from from SAM/BAM
to FASTQ header comment (Chromium 10x Genomics