v3.3.0

How to get abismal

• Linux binary: abismal-3.3.0-Linux.tar.gz
• macOS binary: abismal-3.3.0-macOS.tar.gz
• Source code: abismal-3.3.0.tar.gz

What's changed

• Mapping and indexing now use abismal map and abismal idx instead of the formerly distinct programs.
• Updating the definition of ambiguous mapping reads paired-end.
• Improved performance when many threads are used.

Full Changelog: v3.2.4...v3.3.0

v3.2.4

The correct files to download are abismal-3.2.4.tar.gz or abismal-3.2.4.zip
Please do not download the "Source code" files. Those are generated by GitHub but lack certain files needed to build abismal.

What's Changed

• Preventing attempts to use SSE instruction when not supported by @andrewdavidsmith in #55
• Bugfix for configuring short mode by @andrewdavidsmith in #56

Full Changelog: v3.2.3...v3.2.4

v3.2.3

The correct files to download are abismal-3.2.3.tar.gz or abismal-3.2.3.zip
Please do not download the "Source code" files. Those are generated by GitHub but lack certain files needed to build abismal.

What's Changed

• Option for better mapping of very short reads by @andrewdavidsmith in #47
• Updates for optimizations so that abismal builds on a broader set of (older) compilers @andrewdavidsmith in #52

Full Changelog: v3.2.2...v3.2.3

v3.2.2

The correct files to download are abismal-3.2.2.tar.gz or abismal-3.2.2.zip
Please do not download the "Source code" files. Those are generated by GitHub but lack certain files needed to build abismal.

What's Changed

• Users can specify a set of target regions that are indexed; the rest of the genome is excluded.
• Allows for a gzip compressed genome file when indexing.
• Build system updated to facilitate building binaries for macOS through the Conda.

Full Changelog: v3.2.1...v3.2.2

v3.2.1

The correct files to download are either abismal-3.2.1.zip or abismal-3.2.1.tar.gz
Please do not download the "Source code" files. They are automatically generated by GitHub and incomplete.

What's Changed

• Minor bug fix with progress bar for abismal. Otherwise this version functions the same as v3.2.0.

v3.2.0

The correct files to download are either abismal-3.2.0.zip or abismal-3.2.0.tar.gz
Please do not download the "Source code" files. They are automatically generated by GitHub and incomplete.

What's Changed

• Minor optimizations in local alignment by @andrewdavidsmith in #21
• Added regression tests to run with make check by @andrewdavidsmith in #23
• Improved sensitivity for very low quality paired-end reads, costing up to 3.9% total speed, by @andrewdavidsmith in #25
• Direct BAM format output by @andrewdavidsmith in #27

New Contributors

• @masarunakajima made their first contribution in #20
• @andrewdavidsmith made their first contribution in #21

Full Changelog: v3.1.1...v3.2.0

v3.1.1

The correct files to download are either abismal-3.1.1.zip or abismal-3.1.1.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This is a patch release, as the prior release (v3.1.0) did not properly enable multithreading with some OS/compiler combinations (e.g., macOS with the clang obtained through Xcode).

v3.1.0

The correct files to download are either abismal-3.1.0.zip or abismal-3.1.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This release contains minor optimizations and bug fixes as described below

• abismal was behaving unexpectedly if, by mistake, paired-end read files did not contain the same number of reads. Now it will report an error informing the user should that be the case.
• fixed a couple of cases where reads could be reporting in inconsistent CIGAR lengths.
• if run using verbose (-v), abismal reports the number of threads used, and warns the user if the number of threads requested is more than the number of cores available in the machine.
• some minor optimizations to the banded Smith-Waterman algorithm should make this version run about 5% faster than 3.0.0

v3.0.0

The correct files to download are either abismal-3.0.0.zip or abismal-3.0.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This version of abismal implements new indexing and encoding strategies that will be detailed in a future preprint. It results in faster and more accurate mapping times than 3.0.0.

Please note that your genome indices must be rebuilt to use this new version. Indices built on 2.0.0 or 1.0.0 no longer work

Indexing should take at most 20 mins on a single-core machine for the human genome.

This new release also resolves the following issues:

#5 : abismal now imposes a max read length of 65535 and stops mapping if the user attempts to map a read that is too long.
#8 : we no longer use parallel/algorithm for parallel sorting, so it should be easier to install abismal on OSX machines.

v2.0.0

The correct files to download are either abismal-2.0.0.zip or abismal-2.0.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This version of abismal has several improvements over abismal-1.0.0 (described below). Please note that any index built with 1.0.0 must be rebuilt, as they are not compatible with the current release.

List of changes:

• The new index uses less memory. For hg38, the memory footprint for mapping is reduced from 3.5 GB to 2.7 GB
• Abismal 2.0.0 now performs full alignments
• Abismal 2.0.0 has algorithmic guarantees on exact matches. If a read matches the reference genome exactly somewhere, the match is guaranteed to be found.
• Abismal 2.0.0 is faster in smaller genomes. Search parameters used internally are based on genome k-mer frequencies rather than "hard-coded", which improves speed in genomes like arabidopsis, chicken and bacteria.
• A documentation is now available describing the SAM output format, a detailed description of each parameter and several examples of use.

Some issues are also resolved relative to the previous version:

• 9c93354 : resolves an issue where abismal crashes if a long read is passed to it. If a read is larger than 65535, abismal will report an error message
• the percent_unmapped report now shows 100 minus the percent_mapped (whereas before it showed 100 - percent_unique)
• the error_rate is no longer a percentage, but rather a fraction