Pinned Repositories
GrapeTree
GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
rgi
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
parsnp
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
fastqwiper
An ensemble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving.
betterDays
Transform messy dates to format yyyy-mm-dd
relecov-tools
set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.
relecov_biohackaton
sarscov2-tools
Scripts for analysing SARS-CoV-2 nucleotide sequences
auspice
Web app for visualizing pathogen evolution
CRISPRCasTyper
CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
mlarjim's Repositories
mlarjim/betterDays
Transform messy dates to format yyyy-mm-dd
mlarjim/relecov-tools
set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.
mlarjim/relecov_biohackaton
mlarjim/sarscov2-tools
Scripts for analysing SARS-CoV-2 nucleotide sequences