Alternatives and similar repositories for SKA:

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

• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• marbl / harvest
  ☆52Updated 3 years ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆44Updated last week
• katholt / RedDog
  ☆36Updated 2 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 9 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆26Updated last month
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 8 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆54Updated 5 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆49Updated 6 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 9 months ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆39Updated 2 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆55Updated last week
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆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
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated last year
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆37Updated 3 months ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆26Updated 2 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆48Updated 2 years ago
• 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