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)
| minimap2 | MethylDackel | |
|---|---|---|
| 5 | 1 | |
| 1,688 | 151 | |
| - | - | |
| 7.6 | 3.0 | |
| 7 days ago | 3 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.
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.
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.
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Ask HN: Comment here about whatever you're passionate about at the moment
Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.
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BLAST 10,000 genes?
No experience with this maybe try minimap2(https://github.com/lh3/minimap2) if this doesn't work fall back on blast/blat
- Truncating genome fastas to just overlapping regions
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Alignment of long reads to plasmid and generation of consensus sequence.
You can try minimap2 to align your long reads to your expected plasmid
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Questions about WGS mapping
It sounds like the mapping wasn't very good, you might want to try minimap2 as it is a newer algorithm.
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.
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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 minimap2 and MethylDackel you can also consider the following projects:
bwa-mem2 - The next version of bwa-mem
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
seqtk - Toolkit for processing sequences in FASTA/Q formats
seqstats - Quick summary statistics on fasta/fastq(.gz) files
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
slivar - genetic variant expressions, annotation, and filtering for great good.
hh-suite - Remote protein homology detection suite.
bwa-mem2 - The next version of bwa-mem
bioawk - BWK awk modified for biological data
Klib - A standalone and lightweight C library
celfie - cfDNA cell type of origin estimation