bowtie vs nanopolish

bowtie

An ultrafast memory-efficient short read aligner (by BenLangmead)

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nanopolish

Signal-level algorithms for MinION data (by jts)

Bioinformatics genome-assembly epigenetics methylation Science C++

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bowtie		nanopolish
	Project
1	Mentions	1
252	Stars	541
-	Growth	-
10.0	Activity	5.2
almost 2 years ago	Latest Commit	9 months ago
C++	Language	C++
GNU General Public License v3.0 or later	License	MIT License

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.

bowtie

Posts with mentions or reviews of bowtie. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-09-24.

Burrows–Wheeler Transform
2 projects | news.ycombinator.com | 24 Sep 2022

nanopolish

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

ONT Frustration
1 project | /r/bioinformatics | 9 Apr 2023

I use nanopore for de novo methylation motif detection and some ssDNA signal comparison. Tombo has not worked with R10 data for me, so I’ll have to revisit that. Nanocompore uses Nanopolish for signal comparison, which does not support R10 data (see github).

What are some alternatives?

When comparing bowtie and nanopolish you can also consider the following projects:

bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

megahit - Ultra-fast and memory-efficient (meta-)genome assembler

salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

opensim-core - SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

stellarium - Stellarium is a free GPL software which renders realistic skies in real time with OpenGL. It is available for Linux/Unix, Windows and macOS. With Stellarium, you really see what you can see with your eyes, binoculars or a small telescope.