v0.3.0

Version 0.3.0 provides some bug fixes and algorithmic improvements, but still operates under the same algorithmic structure as 0.2.0. The major changes are

• This version includes some modifications to the algorithm geared toward including accuracy. We also removed some parameters like -c, which are now automatically inferred from the genome. IMPORTANT: Indices must be re-built with this version of abismal. Older indices are no longer compatible.
• Added a -g flag where you can pass the genome directly, so that you don't need a separate indexing step. The program abismalidx is still available, and we recommend indexing reference genomes that will be used multiple times.
• More index statistics are provided during indexing in verbose mode, where the distribution of two-letter k-mers shed light on how heterogeneous the genome is.

Please do download the files named either abismal-0.3.0.tar.gz or abismal-0.3.0.zip. Please do not download the "Source code" files auto-generated by github as they do not contain the necessary files to compile the program.

v0.2.0

This release has major algorithmic improvements to abismal that decrease memory usage and improve accuracy, namely:

(1) minimizers are used as a method to reduce memory usage and disk space in indexing. The shifts parameter no longer exists, as it is fully defined by the minimizer window

(2) more alignments are made in both single- and paired-end mode. In single end, up to 100 valid hits (with >40% edit distance) are aligned. Alignments are not performed if exact matches are found

(3) best candidates are not selected based on edit distance, but on alignment score. Furthermore, if an alignment soft-clip bases, we use the soft-clipped read length as criterion to decide if the read is valid (i.e. passes the minimum threshold to be reported)

v0.1.2

This is the first official release of abismal that generates SAM output in mapping. Please make sure to download either abismal-0.1.2.tar.gz or abismal-0.1.2.zip and not the files that say "Source code" below them.

last-mr-release

This is the last stable release that outputs mr file format

v0.1 - 2020/02/17

This is a frozen stable version of abismal. Some of the improvements to be incorporated in the next release are:

• Aligning PE reads in the select_maps function for all candidate concordant pairs
• Adjust the AbismalAlign.hpp class so it does not adjust the table size dynamically, but rather takes the longest read of a batch to know the memory requirement in advance.
• Decide on ambiguity based on a function of alignment score of first and second best matches.
• Allow for scores to be user-defined in options?