genozip
htslib
| genozip | htslib | |
|---|---|---|
| 2 | 7 | |
| 149 | 775 | |
| - | 1.5% | |
| 9.1 | 8.9 | |
| 14 days ago | 4 days ago | |
| C | C | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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genozip
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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
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?
BEETL - BEETL
seqtk - Toolkit for processing sequences in FASTA/Q formats
snappy - Helps you browse through and interpret your genotype data
bwa-mem2 - The next version of bwa-mem
sambamba - Tools for working with SAM/BAM data
cyvcf2 - cython + htslib == fast VCF and BCF processing
zstd - Zstandard - Fast real-time compression algorithm
aws-genomics-workflows - Genomics Workflows on AWS
tamtools - Create and manage hybrid reference assemblies to consolidate two original DNA alignments against different reference assemblies.
libdna - ♥ Essential Functions for DNA Manipulation
community - An open community with an interest in developing and using new technologies for tensor data storage.
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite