GenomeWorks v0.5.0
Release v0.5.0 brings major performance and functionality updates to all modules with a focus on improved handling of long read sequences.
- Clara Genomics Analysis -> GenomeWorks
- As of this release, the repository name and associated project and package names have been updated to
GenomeWorks. The python bindings package is now available on PyPI asgenomeworks.
- CUDA Partial Order Aligner (CUDA POA)
- Novel adaptive banding implementation for partial order alignment achieves measurably better accuracy than default static band parameters with marginal drop in performance.
- Support for consensus and MSA of long read sequences in all accuracy modes (full matrix, adaptive band and static band).
- Several bug fixes and general stability improvements.
- Backwards incompatible API changes.
- CUDA Aligner
- New banded Myers algorithm with compact memory footprint and adjustable band size accelerates
cudaalignerperformance of long read global alignment (10-15kb sequences) by ~3x over previous implementations with comparable accuracy. Narrow bands may lead to non-optimal alignments. - Updated
Alignmentobject provides edit distance for each alignment and a new flag to signal optimal vs non-optimal alignments. - Bug fixes and improved test coverage.
- Backward incompatible API changes.
- CUDA Mapper
- New conditions for fusing overlaps and changes to default parameters improve accuracy on small genomes without genomic repeats (NG50, mismatches, and indel accuracy matching minimap2 for E. coli and S. aureus).
- Saving copies of indices in host memory and transferring them to device memory on demand avoids both additional index generations and leaves sufficient device memory for matcher and overlapper
- Using CUB-based search algorithm gets better performance than Thrust because it leverages additional information about the data that is to be sorted.
- New sample showcasing the use of
cudamapperAPIs to build a GPU-accelerated, minimizer based mapper.