MMseqs2
MethylDackel
MMseqs2 | MethylDackel | |
---|---|---|
4 | 1 | |
1,268 | 153 | |
2.6% | - | |
7.7 | 3.0 | |
7 days ago | 3 months ago | |
C | C | |
GNU General Public License v3.0 only | MIT License |
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MMseqs2
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Clustering tool that could help cluster protein sequences based on percentage identity
A tool I often recommend for sequence clustering is mmseqs2 : https://github.com/soedinglab/MMseqs2, fast and efficient :)
- MMseqs2 – an example of great software for biology
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Metagenomics: abundances of short reads using genome databases
Tools like the the mmseqs2 "taxonomy" module, or DIAMOND v2, can efficiently align contigs to genome databases to assign taxonomy, but it seems like they aren't intended to provide abundance estimates for each taxon (since that would require mapping reads, and mmseqs2 can't even use paired-reads). Can anyone recommend tools or methods for A) connecting per-contig coverage information to contig taxonomy, or B) mapping short reads against genome databases?
- Retrieving One-to-One Orthologs of Unprocessed cDNAs
MethylDackel
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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?
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
hh-suite - Remote protein homology detection suite.
seqtk - Toolkit for processing sequences in FASTA/Q formats
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
SqueezeMeta - A complete pipeline for metagenomic analysis
bioawk - BWK awk modified for biological data
celfie - cfDNA cell type of origin estimation