samtools
libBigWig
| samtools | libBigWig | |
|---|---|---|
| 3 | 1 | |
| 1,549 | 70 | |
| 1.0% | - | |
| 8.6 | 0.0 | |
| 5 days ago | over 1 year ago | |
| C | C | |
| GNU General Public License v3.0 or later | MIT License |
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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
libBigWig
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Technical specification for the bigWig file format
And that is using libBigWig which specifically references Kent Utils.
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
bbi-js - Parser for bigwig and bigbed files
RNAlien - RNAlien - unsupervised RNA family model construction
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
memexml - Haskell cabal libary for parsing Meme motif finder xml output
FormalGrammars - Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)