aws-genomics-workflows
htslib
aws-genomics-workflows | htslib | |
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1 | 7 | |
136 | 775 | |
- | 1.5% | |
0.0 | 8.9 | |
9 months ago | 6 days ago | |
Shell | C | |
MIT No Attribution | GNU General Public License v3.0 or later |
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aws-genomics-workflows
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Tips for scalable workflows on AWS
There are a lot of tools built with C/C++ using glibc shared libraries. The AWS CLI v2 is one of these tools. It is common for workflow engines running on AWS to bind mount the AWS CLI from the host instance into the container so that it is available for interacting with other AWS services like staging data from Amazon S3. Challenges arise when a tooling container is based on an image without glibc shared libraries as is the case with ultra-minimal base images like alpine and busybox. You can still use these ultra-minimal images, but you need to take extra steps to ensure that glibc shared libraries are available. For example, the AWS CLI v2 is distributed with the shared libraries it needs, and to make it work on an alpine based container, you can modify the LD_LIBRARY_PATH environment variable in the container environment to point to where these shared libraries are installed.
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?
github-slug-action - GitHub Action to expose slug value of GitHub environment variables inside your GitHub workflow
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
hello-github-actions - Create a GitHub Action and use it in a workflow.
seqtk - Toolkit for processing sequences in FASTA/Q formats
aws-sdk - Landing page for the AWS SDKs on GitHub
bwa-mem2 - The next version of bwa-mem
Image-Optimizer-Action - A Github Action to optimize / compress images in your repository
cyvcf2 - cython + htslib == fast VCF and BCF processing
ci-workflows-flutter - Contains all CI Workflows for Flutter applications
libdna - ♥ Essential Functions for DNA Manipulation
OCR-PDF-Action - A GitHub action for turning scanned PDF's into searchable documents
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite