octopus
bwa-mem2
octopus | bwa-mem2 | |
---|---|---|
1 | 2 | |
296 | 677 | |
0.3% | 1.0% | |
4.0 | 2.6 | |
9 months ago | 5 months ago | |
C++ | C++ | |
MIT License | GNU General Public License v3.0 or later |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
octopus
-
genotyping tool
Check out octopus https://github.com/luntergroup/octopus
bwa-mem2
-
Anyone use DRAGEN-GATK?
If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
-
Software Development Project
I’ve recently switched to bwa mem2 and the speed increase is nice for what is basically a drop in replacement (after a bit of validation to make sure that was true). https://github.com/bwa-mem2/bwa-mem2
What are some alternatives?
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
bowtie2 - A fast and sensitive gapped read aligner
rare-disease-wf - (WIP) best-practices workflow for rare disease
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
htslib - C library for high-throughput sequencing data formats
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
vg - tools for working with genome variation graphs
GenomicSQLite - Genomics Extension for SQLite
seqstats - Quick summary statistics on fasta/fastq(.gz) files