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v0.2.0

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@guilhermesena1 guilhermesena1 released this 08 Apr 05:36
· 376 commits to master since this release

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)