Alternatives and similar repositories for scoary-2:

Users that are interested in scoary-2 are comparing it to the libraries listed below

• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆44Updated 2 weeks ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 5 months ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated 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
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆18Updated last year
• 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
  ☆37Updated 2 weeks ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆56Updated 2 weeks ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆33Updated last month
• 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
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆23Updated 8 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆38Updated 5 months ago
• ablab / metaGT
  Pipeline for metagenome and metatranscriptome joint assembly
  ☆20Updated 2 years ago
• michaelkyu / PlasX
  PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture
  ☆33Updated 3 years ago
• AnantharamanLab / PropagAtE
  Prophage Activity Estimator
  ☆26Updated 9 months ago
• wandreopoulos / deeplasmid
  ☆20Updated 6 months ago
• AlexanderLabWHOI / EukHeist
  ☆25Updated last year
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆19Updated 2 years ago
• cjneely10 / EukMetaSanity
  Structural and functional annotation of eukaryotic metagenome-assembled genomes
  ☆22Updated last year
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆32Updated 5 months ago
• wbazant / CORRAL
  ☆13Updated last year
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last year
• valflanza / accnet
  ☆13Updated 7 years ago
• boulund / phaster_scripts
  Small utility script to submit genomes to PHASTER for phage detection
  ☆23Updated 3 years ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 8 months ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 11 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 3 months ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year