Alternatives and similar repositories for scripts

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

• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 7 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆28Updated this week
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 4 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated 2 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 3 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 2 weeks ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated 2 months ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆21Updated 2 years ago
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆45Updated 3 weeks ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated 3 weeks ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆33Updated 5 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated last year
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆24Updated 9 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 6 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated last month
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆38Updated last month
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆55Updated last month
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆24Updated 2 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆64Updated 2 years ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆32Updated last year
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last month
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆48Updated 2 years ago