FormalGrammars vs samtools

FormalGrammars

Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL) (by choener)

Specific Industries Bioinformatics

Source Code

bioinf.uni-leipzig.de

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samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data (by samtools)

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Source Code

htslib.org

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FormalGrammars		samtools
	Project
-	Mentions	3
5	Stars	1,546
-	Growth	2.3%
0.0	Activity	8.4
over 1 year ago	Latest Commit	7 days ago
Haskell	Language	C
GNU General Public License v3.0 only	License	GNU General Public License v3.0 or later

The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.

FormalGrammars

Posts with mentions or reviews of FormalGrammars. We have used some of these posts to build our list of alternatives and similar projects.

We haven't tracked posts mentioning FormalGrammars yet.
Tracking mentions began in Dec 2020.

samtools

Posts with mentions or reviews of samtools. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-10-18.

BWA MEM with merged paired-end reads and unmerged in the same run.
1 project | /r/bioinformatics | 13 Jun 2023

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)
Show a Tanuki with Samtools!
2 projects | dev.to | 18 Oct 2022

In this post, I'm going to add the command tanuki to Samtools to display a ASCII art(AA) tanuki.
How do I know if I'm gonna get my module?
1 project | /r/nus | 7 Jan 2022

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?

When comparing FormalGrammars and samtools you can also consider the following projects:

ViennaRNAParser

seqtk - Toolkit for processing sequences in FASTA/Q formats

taxonomy - An open source application built using the new router, server components and everything new in Next.js 13.

MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite

RNAlien - RNAlien - unsupervised RNA family model construction

cmv - Visualize HMMs, CMs and their comparisons

libBigWig - A C library for handling bigWig files

vcf - Haskell library to handle VCF (Variant Call Format) files

libdna - ♥ Essential Functions for DNA Manipulation

Taxonomy - Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources.

htslib - C library for high-throughput sequencing data formats