cyvcf2
htslib
| cyvcf2 | htslib | |
|---|---|---|
| 1 | 7 | |
| 358 | 776 | |
| - | 1.7% | |
| 7.7 | 8.9 | |
| 2 months ago | 7 days ago | |
| Cython | C | |
| MIT License | GNU General Public License v3.0 or later |
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cyvcf2
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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
htslib
- 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?
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
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
chatnoir-resiliparse - A robust web archive analytics toolkit
seqtk - Toolkit for processing sequences in FASTA/Q formats
truvari - Structural variant toolkit for VCFs
bwa-mem2 - The next version of bwa-mem
hts.cr - HTSlib bindings for Crystal
aws-genomics-workflows - Genomics Workflows on AWS
ruby-htslib - HTSlib bindings for Ruby
libdna - ♥ Essential Functions for DNA Manipulation
Hail - Cloud-native genomic dataframes and batch computing
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite