Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species
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Updated
Jun 12, 2024 - Java
Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species
Unified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)
estimating the genome size from illumina genome-seq and plotting the genome size.
genotype prepare for sequencing paltform.
graphanalyzer python package for dealing with paf and gfa alignments.
A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.
MAGset is a tool to analyze and compare MAGs of known species
A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Repository for the TRANSIT and TPP tools developed by the Ioerger Lab
R code in R Markdown used for ucm genomes and genome analysis course
Teaching materials for SymbNET course: from MAGs to GEMs
Arche: a functional-optimized annotator for microbial meta(genomes)
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