hts.cr
samtools
| hts.cr | samtools | |
|---|---|---|
| 1 | 3 | |
| 10 | 1,549 | |
| - | 1.0% | |
| 5.9 | 8.6 | |
| 3 months ago | 6 days ago | |
| Crystal | 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.
hts.cr
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Show a Tanuki with Samtools!
First, let's make sure that Samtools can be built successfully. Note that the build requires htslib and other dependencies. In my case, I put htslib directory in the same directory as samtools because I build htslib by myself for htslib binding of Crystal language which I make for my personal interest. If you put htslib here, samtools can detect it automatically. htslib requires submodules git submodule update -i --recursive. If you get stuck, please google it. It would be safer to check out a stable tag git checkout 1.16.1, and switch to a new branch git switch tanuki. It is up to you.
samtools
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BWA MEM with merged paired-end reads and unmerged in the same run.
I don’t know about your first question, but for your second, use “bwa mem -p …” for smart pairing of an interleaved FASTQ/A with both paired end reads and singletons. BWA will recognize whether adjacent reads are paired if they have the same prefix (see here)
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Show a Tanuki with Samtools!
In this post, I'm going to add the command tanuki to Samtools to display a ASCII art(AA) tanuki.
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How do I know if I'm gonna get my module?
Quite a number of bioinformatics related tool that were written in C/C++, eg. (https://github.com/samtools/samtools). But there are also a lot of modern packages for Python / R now
What are some alternatives?
cyvcf2 - cython + htslib == fast VCF and BCF processing
seqtk - Toolkit for processing sequences in FASTA/Q formats
zstd.cr - Crystal bindings to the Zstandard (zstd) compression library
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
sambamba - Tools for working with SAM/BAM data
RNAlien - RNAlien - unsupervised RNA family model construction
libBigWig - A C library for handling bigWig files
libdna - ♥ Essential Functions for DNA Manipulation
htslib - C library for high-throughput sequencing data formats
bioinformatics-toolkit - A collection of bioinformatics algorithms
BlastHTTP - Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice
ClustalParser - Parse output of Clustal tools