Alternatives and similar repositories for pgcgap:

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

• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated 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
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆25Updated 2 years ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆23Updated 6 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 8 months ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆26Updated 2 months ago
• chmccarthy / Pangloss
  Pangenome analysis of eukaryotes.
  ☆18Updated 4 years ago
• gatech-genemark / MetaGeneMark-2
  MetaGeneMark-2: Improved Gene Prediction in Metagenomes
  ☆18Updated 10 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆37Updated 3 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last year
• sheppardlab / pGWAS
  pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria
  ☆11Updated 6 years ago
• wandreopoulos / deeplasmid
  ☆18Updated 4 months ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆40Updated last week
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated last week
• 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 last year
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆35Updated 3 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆52Updated last month
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• spencer411 / FastANI_heatmap
  This repository contains R code for building a heatmap and histogram with the output of FastANI
  ☆16Updated 3 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• LorMeBioAI / MBPD
  ☆15Updated last month
• patrickwest / EukRep_Pipeline
  ☆24Updated 6 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆26Updated last month
• feargalr / Demovir
  Taxonomic classification of viruses at Order and Family level
  ☆19Updated last year
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 9 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆51Updated 4 years ago