Alternatives and similar repositories for SKA

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

• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated last month
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• katholt / RedDog
  ☆37Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last month
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆30Updated 9 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• zheminzhou / EToKi
  all methods related to Enterobase
  ☆43Updated last year
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆41Updated last week
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 2 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆34Updated 6 years ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated 2 years ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 2 weeks ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆61Updated 7 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆92Updated 2 months ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆63Updated 3 months ago
• virus-evolution / gofasta
  ☆36Updated 5 months ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last week
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆27Updated 6 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago