Alternatives and similar repositories for MLSTar:

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

• larssnip / micropan
  R package for microbial pangenomics
  ☆21Updated 2 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆48Updated 2 years ago
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 6 years ago
• KasperSkytte / mmgenome2
  Tools for extracting individual genomes from metagenomes
  ☆17Updated last year
• cchauve / HyAsP
  Hybrid Assembler for Plasmids
  ☆10Updated 2 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 6 years ago
• aweimann / traitar
  ☆22Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆24Updated 2 months ago
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆20Updated last year
• Arcadia-Science / sourmashconsumr
  Working with the outputs of sourmash in R
  ☆26Updated last year
• emvolz / treedater
  Scalable relaxed clock phylogenetic dating
  ☆24Updated 10 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• SWittouck / tidyamplicons
  Functions to manipulate and visualize microbial community data
  ☆11Updated last year
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆22Updated 6 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆20Updated 3 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 6 months ago
• valflanza / accnet
  ☆13Updated 7 years ago
• ewissel / hAMRoaster
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Updated 10 months ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆11Updated 10 months ago
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆17Updated last year
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• davised / get_assemblies
  Download assembly files from NCBI
  ☆11Updated last year
• lmlui / Jorg
  MAG Circularization Method
  ☆33Updated 2 years ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆12Updated 7 months ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆24Updated 9 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• klebgenomics / Kaptive
  ☆44Updated 2 weeks ago
• nick-youngblut / traitar3
  From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)
  ☆22Updated 6 months ago