|14 days ago||about 1 year ago|
|GNU General Public License v3.0 or later||GNU General Public License v3.0 or later|
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sqzlib - kseq compatible DNA fastA/Q encoding and compression library
5 projects | reddit.com/r/bioinformatics | 21 Nov 2021
Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.
What are some alternatives?
bwa-mem2 - The next version of bwa-mem
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
bowtie2 - A fast and sensitive gapped read aligner
Klib - A standalone and lightweight C library
sqzlib - Blocked bases fastX encoding and compression
seqstats - Quick summary statistics on fasta/fastq(.gz) files
GenomicSQLite - Genomics Extension for SQLite
megahit - Ultra-fast and memory-efficient (meta-)genome assembler