biostar-central
htslib
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biostar-central | htslib | |
---|---|---|
10 | 7 | |
573 | 772 | |
- | 2.1% | |
2.5 | 9.0 | |
14 days ago | 7 days ago | |
Python | C | |
MIT License | GNU General Public License v3.0 or later |
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.
biostar-central
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Forums/Communites for Bioinformatics on Other Platforms?
Biostars is a great community, basically a bioinformatics-focused version of stackoverflow.
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Good resource to learn coding for molecular biology? Or places where I can access real data sets for analysis and practice?
Go here: https://www.biostars.org/
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Is there a forum for clinical informatics that does what biostars does for bioinformatics?
Biostars (https://www.biostars.org/) Q and A forum for questions about bioinformatic tasks like alignment, differential expression analysis, etc., organized in a vaguely stack overflow like way.
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Demoralized and dejected, the job market only seems to be getting worse.
Other place to get suggestions and padding for your Git repo would be to look at questions on boards like BioStars or StackExchange Implement, test, push, and comment with your solution. Make sure you all follow proper coding conventions too. Folks not only want the right answer they want to understand how it's done
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first stop codon
also consider posting bioinformatics questions over at https://www.biostars.org/ instead of reddit
- Does anyone know of a repository for actual genetic data?
- Ask HN: HN, but for Scientists?
- Where do Data Analyst and Data Science ask question most of the time (except StackOverflow and StackExchange)?
- Scientists Are Finding Fungi in Cancerous Tumors
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Ask HN: Any open source stack exchange clone
In the bioinformatics sphere there is this MIT-licensed Stack Exchange clone: https://github.com/ialbert/biostar-central
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?
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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
qpixel - Q&A-based community knowledge-sharing software
seqtk - Toolkit for processing sequences in FASTA/Q formats
sra-tools - SRA Tools
bwa-mem2 - The next version of bwa-mem
Lobsters - Computing-focused community centered around link aggregation and discussion
cyvcf2 - cython + htslib == fast VCF and BCF processing
aws-genomics-workflows - Genomics Workflows on AWS
question2answer - Question2Answer is a free and open source platform for Q&A sites, running on PHP/MySQL.
libdna - ♥ Essential Functions for DNA Manipulation