Alternatives and similar repositories for scripts

Users that are interested in scripts are comparing it to the libraries listed below

• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆45Updated 3 months ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆25Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆28Updated 7 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 6 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last month
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆25Updated last week
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆22Updated 2 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆31Updated last month
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• CFIA-NCFAD / wgscovplot
  The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…
  ☆19Updated last year
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 10 months ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated last month
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆63Updated 4 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆41Updated last week
• lmlui / Jorg
  MAG Circularization Method
  ☆32Updated 3 years ago
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆27Updated last week
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆62Updated last month
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆70Updated 2 months ago
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆15Updated 2 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 5 years ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆13Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago