Alternatives and similar repositories for bactmap

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

• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 5 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last month
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆38Updated 8 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆45Updated last month
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated 4 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 3 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
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆42Updated this week
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated 2 years ago
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆37Updated last week
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆36Updated 2 months ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 9 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆28Updated 6 months ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆85Updated 2 months ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆59Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 5 months ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆35Updated 9 months ago