Alternatives and similar repositories for charcoal:

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

• AlexanderLabWHOI / EUKulele
  Automatic eukaryotic taxonomic classification
  ☆28Updated last month
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last month
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆44Updated this week
• tseemann / scapper
  Whole genome core alignments from multiple draft genomes
  ☆13Updated 8 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated this week
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 2 weeks ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated this week
• functional-dark-side / agnostos-wf
  ☆45Updated last year
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 6 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated last month
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 4 months ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆48Updated 3 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆39Updated 5 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆37Updated 2 weeks ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆42Updated 5 months ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆23Updated 9 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• adamhockenberry / bacphlip
  A python library for predicting phage lifestyle based on genome sequence
  ☆37Updated last year
• Shamir-Lab / SCAPP
  SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…
  ☆31Updated 2 years ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated last week
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated last year
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• wslh-bio / spriggan
  Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
  ☆16Updated last week
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆27Updated 2 months ago
• dib-lab / genome-grist
  map Illumina metagenomes to genomes!
  ☆38Updated 3 weeks ago