genozip
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too (by divonlan)
sambamba
Tools for working with SAM/BAM data (by biod)
| genozip | sambamba | |
|---|---|---|
| 2 | 1 | |
| 149 | 553 | |
| - | 0.2% | |
| 9.1 | 6.5 | |
| 14 days ago | 9 months ago | |
| C | D | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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.
genozip
Posts with mentions or reviews of genozip.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-01-09.
-
We're wasting money by only supporting gzip for raw DNA files
You might want to check out Genozip - a modern compressor for FASTQ, BAM/CRAM, VCF etc.
- Introducing Genozip - a file compressor for BAM, FASTQ, VCF etc
sambamba
Posts with mentions or reviews of sambamba.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-12-14.
-
where to start?
Yeah the D programming language, https://dlang.org/ one of my favorite languages to program in. It's unfortunately not used a lot in bioinformatics, and deserves more attention in my opinion. E.g. sambamba for working with sam/bam files is written in it (https://github.com/biod/sambamba) it's one of the most performant tools for working with NGS data because it uses async io and fibers.
What are some alternatives?
When comparing genozip and sambamba you can also consider the following projects:
htslib - C library for high-throughput sequencing data formats
bam-filter - Use simple expressions to filter a BAM/CRAM file
BEETL - BEETL
ruby-htslib - HTSlib bindings for Ruby
snappy - Helps you browse through and interpret your genotype data
swirl - :cyclone: Learn R, in R.
zstd - Zstandard - Fast real-time compression algorithm
hts.cr - HTSlib bindings for Crystal
tamtools - Create and manage hybrid reference assemblies to consolidate two original DNA alignments against different reference assemblies.
dmd - dmd D Programming Language compiler
community - An open community with an interest in developing and using new technologies for tensor data storage.