bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) (by lh3)
MethylDackel
A (mostly) universal methylation extractor for BS-seq experiments. (by dpryan79)
| bwa | MethylDackel | |
|---|---|---|
| 3 | 1 | |
| 1,453 | 151 | |
| - | - | |
| 2.7 | 3.0 | |
| 18 days ago | 3 months ago | |
| C | C | |
| GNU General Public License v3.0 only | 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.
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.
bwa
Posts with mentions or reviews of bwa.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-25.
-
my friend showed me his code, thees are all functions
Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h
- Scientists Are Finding Fungi in Cancerous Tumors
- Burrows–Wheeler Transform
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
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 bwa and MethylDackel you can also consider the following projects:
foldseek - Foldseek enables fast and sensitive comparisons of large structure sets.
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
slivar - genetic variant expressions, annotation, and filtering for great good.
seqtk - Toolkit for processing sequences in FASTA/Q formats
sra-tools - SRA Tools
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
bowtie - An ultrafast memory-efficient short read aligner
hh-suite - Remote protein homology detection suite.
spades - SPAdes Genome Assembler
bioawk - BWK awk modified for biological data
libBigWig - A C library for handling bigWig files
celfie - cfDNA cell type of origin estimation