ABySS 2.1.0 (Apr 13, 2018)


This release adds support for misassembly correction and scaffolding using linked reads, using Tigmint and ARCS. (Tigmint and ARCS must be installed separately.) In addition, simultaneous optimization of `s` (seed length) and `n` (min supporting read pairs / Chromium barcodes) is now supported during scaffolding.

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

Available downloads

source code

For all platforms

Change log

* Fix hang on input SAM containing no alignments with MAPQ > 0

* New `lr` parameter. Provide linked reads (i.e. 10x Genomics
Chromium reads) via this parameter to perform misassembly
correction and scaffolding using Chromium barcode information.
Requires Tigmint and ARCS tools to be installed in addition
to ABySS.
* Fix bug where `j` (threads) was not being correctly passed to
to `bgzip`/`pigz`
* Fix bug where `zsh` time/memory profiling was not being used,
even when `zsh` was available

* Simultaneous optimization of `n` and `s` using line search
or grid search [default]

* add options `-s` and `-n` to filter paired-end paths by
seed length and edge weight, respectively