htslib
cyvcf2
| htslib | cyvcf2 | |
|---|---|---|
| 7 | 1 | |
| 775 | 357 | |
| 1.5% | - | |
| 8.9 | 7.7 | |
| 6 days ago | 2 months ago | |
| C | Cython | |
| GNU General Public License v3.0 or later | MIT License |
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.
htslib
- Gentoo -Os vs -O3 application startup time?
- Does anyone know of a repository for actual genetic data?
-
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
-
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:
-
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
-
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.
-
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.
cyvcf2
-
How can I index and query my VCF files by an INFO tag?
If you in command line, bcftools. If in python, https://github.com/brentp/cyvcf2
What are some alternatives?
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
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
seqtk - Toolkit for processing sequences in FASTA/Q formats
chatnoir-resiliparse - A robust web archive analytics toolkit
bwa-mem2 - The next version of bwa-mem
truvari - Structural variant toolkit for VCFs
aws-genomics-workflows - Genomics Workflows on AWS
hts.cr - HTSlib bindings for Crystal
libdna - ♥ Essential Functions for DNA Manipulation
ruby-htslib - HTSlib bindings for Ruby
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
Hail - Cloud-native genomic dataframes and batch computing