Alternatives and similar repositories for strainy

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

• bvalot / pyMLST
  whole genome MLST analysis
  ☆43Updated 2 weeks ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆42Updated 7 months ago
• bcgsc / ntSynt
  Detecting multi-genome synteny using minimizer graph mapping
  ☆78Updated last month
• DessimozLab / FastOMA
  FastOMA is a scalable software package to infer orthology relationship.
  ☆76Updated last week
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆49Updated 3 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆87Updated 4 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• EBI-Metagenomics / mobilome-annotation-pipeline
  ☆51Updated 3 weeks ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆54Updated last month
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 9 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 3 months ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆48Updated 2 weeks ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• mourisl / centrifuger
  Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.
  ☆59Updated this week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• metashot / awemags
  aweMAGs: a fully automated workflow for eukariotic MAGs
  ☆16Updated 2 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 4 months ago
• epi2me-labs / wf-16s
  ☆31Updated 2 months ago
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆41Updated 3 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• bcgsc / ntEdit
  ✏️ Genome assembly polishing & SNV detection
  ☆68Updated 4 months ago
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆49Updated last year
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago