TASR 1.6 (Jan 01, 2016)


Initial Bloom filter implementation. Better prefix-tree handling. Whole pair recruitment leading to longer, more specific contigs.

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For all platforms (378.3 KB)

Release Notes

State Final release
License GPL
Release Manager Rene Warren

1) Bloom filter functionality to exclude k-mers from your sequence target space (TASR-Bloom). This could be useful for removing repeats and, for example, unwanted ERV elements.

TASR and TASR-Bloom:
2) 4-base encoding of the first 16 bases of each read while populating a 4-nodes (16/4) prefix tree.

3) The new (and required) coverage depth threshold -w option, gives users more control over the assembly, focusing on higher-depth contigs and ignoring short, low-depth contigs comprised of NGS reads having errors, contaminating reads or any other (perhaps unwanted) sequences.

4) Improvements to read recruitment from sorted-by-name bam files, recruiting whole read pairs when at least one read has a target seed k-mer match. This has the potential to extend the reconstructed contigs by 2X the library fragment size (upstream and downstream) of the target sequence.

Project Resources

Project owner: Rene Warren