Alternatives and similar repositories for EBAME18

Users that are interested in EBAME18 are comparing it to the libraries listed below

• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆78Updated 4 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 5 years ago
• katholt / RedDog
  ☆37Updated 3 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆61Updated 2 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆67Updated 3 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆35Updated last year
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆50Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆65Updated 7 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 3 months ago
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆43Updated 4 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆33Updated 6 years ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆41Updated 3 months ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆32Updated 9 months ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 3 years ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆54Updated 3 months ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆25Updated 7 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 5 years ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated 2 weeks ago
• chjp / ANI
  Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes
  ☆18Updated 3 years ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 5 months ago
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆63Updated 4 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆59Updated last month
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 3 weeks ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆80Updated 2 years ago