ruby-htslib
HTSlib bindings for Ruby (by kojix2)
htslib
C library for high-throughput sequencing data formats (by samtools)
| ruby-htslib | htslib | |
|---|---|---|
| 1 | 7 | |
| 8 | 775 | |
| - | 1.5% | |
| 7.4 | 8.9 | |
| 3 months ago | 3 days ago | |
| Ruby | C | |
| MIT License | GNU General Public License v3.0 or later |
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.
ruby-htslib
Posts with mentions or reviews of ruby-htslib.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-07-26.
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ffi-bitfield
I'm working on a bioinformatics-related binding called ruby-htslib. htslib makes heavy use of bit fields throughout the library, so supporting bit fields is inevitable.
htslib
Posts with mentions or reviews of htslib.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-29.
- Gentoo -Os vs -O3 application startup time?
- Does anyone know of a repository for actual genetic data?
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Pigz: A parallel implementation of gzip for multi-core machines
There is another nice multi-core gzip based library called BGZF[1]. It is commonly used in bioinformatics. BGZF has the added advantage that it is block compressed with built in indexing method to permit seeking in compressed files.
[1] https://github.com/samtools/htslib
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Tips for scalable workflows on AWS
In contrast, processing can start immediately and only transfer what is necessary if tooling can read bytes of data directly from Amazon S3. Tools based on htslib can do this, so you can run something like:
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Software Development Project
Another idea is add in reading cloud data natively e.g. htslib which samtools relies on can read s3 directly. https://github.com/samtools/htslib
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Interested in Bioinformatics / C pair-programming opportunity / learning / portfolio project.
Greetings! I'm a bioinformatics software dev in San Francisco and I'm looking for others interested in working on a high-performance genetic data analysis project. The project is in C, using https://github.com/samtools/htslib.
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ffi-bitfield
I'm working on a bioinformatics-related binding called ruby-htslib. htslib makes heavy use of bit fields throughout the library, so supporting bit fields is inevitable.
What are some alternatives?
When comparing ruby-htslib and htslib you can also consider the following projects:
ffi - Ruby FFI
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
cyvcf2 - cython + htslib == fast VCF and BCF processing
seqtk - Toolkit for processing sequences in FASTA/Q formats
ffi-bitfield - Bit field for Ruby-FFI
bwa-mem2 - The next version of bwa-mem
sambamba - Tools for working with SAM/BAM data
aws-genomics-workflows - Genomics Workflows on AWS
libdna - ♥ Essential Functions for DNA Manipulation
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data