minimap2 VS MethylDackel

Compare minimap2 vs MethylDackel and see what are their differences.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)

MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments. (by dpryan79)
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minimap2 MethylDackel
5 1
1,672 151
- -
7.8 3.0
9 days ago 2 months ago
C C
GNU General Public License v3.0 or later 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.
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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.

minimap2

Posts with mentions or reviews of minimap2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-11-06.

MethylDackel

Posts with mentions or reviews of MethylDackel. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-06-08.
  • WGBS normalization methods inquiry
    2 projects | /r/bioinformatics | 8 Jun 2022
    Anyway, I'm curious if there are methods used to normalize the data to account for the difference in sequencing depth. I've already employed random subsampling like they used in the EpiQC study to achieve a similar mean coverage across the board, but I'm curious if there are any other known methods which minimize information loss. For context, I won't be doing DML/DMR detection (I know these methods can take coverage into account when merging DMRs and performing statistical analyses), but rather tissue of origin estimation between sets. My data are per-CpG context bedGraph files from MethylDackel, but I have access to the per-Cytosine bedGraphs all the way up to the raw FASTQ files.

What are some alternatives?

When comparing minimap2 and MethylDackel you can also consider the following projects:

bwa-mem2 - The next version of bwa-mem

slivar - genetic variant expressions, annotation, and filtering for great good.

seqtk - Toolkit for processing sequences in FASTA/Q formats

seqstats - Quick summary statistics on fasta/fastq(.gz) files

bwa-mem2 - The next version of bwa-mem

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

Klib - A standalone and lightweight C library

biowasm - WebAssembly modules for genomics

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

Bitgrid - Bitgrid - a new model of computation

bioawk - BWK awk modified for biological data