GenomicSQLite
bwa-mem2
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GenomicSQLite | bwa-mem2 | |
---|---|---|
1 | 2 | |
152 | 674 | |
- | 1.5% | |
3.4 | 2.6 | |
3 months ago | 4 months ago | |
C++ | C++ | |
Apache License 2.0 | GNU General Public License v3.0 or later |
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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.
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).
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
What are some alternatives?
hap.py - Haplotype VCF comparison tools
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
FlatBuffers - FlatBuffers: Memory Efficient Serialization Library
bowtie2 - A fast and sensitive gapped read aligner
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
seq - A high-performance, Pythonic language for bioinformatics
htslib - C library for high-throughput sequencing data formats
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