hts.cr
HTSlib bindings for Crystal (by bio-cr)
sambamba
Tools for working with SAM/BAM data (by biod)
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| hts.cr | sambamba | |
|---|---|---|
| 1 | 1 | |
| 10 | 554 | |
| - | 0.9% | |
| 5.9 | 6.5 | |
| 3 months ago | 8 months ago | |
| Crystal | D | |
| MIT License | 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.
hts.cr
Posts with mentions or reviews of hts.cr.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-18.
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Show a Tanuki with Samtools!
First, let's make sure that Samtools can be built successfully. Note that the build requires htslib and other dependencies. In my case, I put htslib directory in the same directory as samtools because I build htslib by myself for htslib binding of Crystal language which I make for my personal interest. If you put htslib here, samtools can detect it automatically. htslib requires submodules git submodule update -i --recursive. If you get stuck, please google it. It would be safer to check out a stable tag git checkout 1.16.1, and switch to a new branch git switch tanuki. It is up to you.
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.
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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 hts.cr and sambamba you can also consider the following projects:
cyvcf2 - cython + htslib == fast VCF and BCF processing
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
zstd.cr - Crystal bindings to the Zstandard (zstd) compression library
bam-filter - Use simple expressions to filter a BAM/CRAM file
ruby-htslib - HTSlib bindings for Ruby
swirl - :cyclone: Learn R, in R.
dmd - dmd D Programming Language compiler
htslib - C library for high-throughput sequencing data formats