bwa-mem2
GenomicSQLite
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| bwa-mem2 | GenomicSQLite | |
|---|---|---|
| 2 | 1 | |
| 674 | 152 | |
| 1.5% | - | |
| 2.6 | 3.4 | |
| 4 months ago | 3 months ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
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.
bwa-mem2
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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.
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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
GenomicSQLite
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sqlite-zstd: Transparent dictionary-based row-level compression for SQLite - An SQLite extension written in Rust to reduce the database size without losing functionality
Yes, that is indeed an obviously missing part. I knew about ZIPVFS, but somehow forgot to investigate closer. Probably because I started this project before GenomicsSQLite was a thing (that seems like the best alternative).
What are some alternatives?
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
hap.py - Haplotype VCF comparison tools
bowtie2 - A fast and sensitive gapped read aligner
FlatBuffers - FlatBuffers: Memory Efficient Serialization Library
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
htslib - C library for high-throughput sequencing data formats
seq - A high-performance, Pythonic language for bioinformatics
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
seqstats - Quick summary statistics on fasta/fastq(.gz) files
vg - tools for working with genome variation graphs
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites