Alternatives and similar repositories for SKA:

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

• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• katholt / RedDog
  ☆36Updated 2 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 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 10 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 10 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 9 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated last week
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆58Updated this week
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last year
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 2 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆38Updated 4 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆56Updated last month
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 7 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated last year
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆27Updated 2 months ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆52Updated 10 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated this week