Alternatives and similar repositories for LatentStrainAnalysis:

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

• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆48Updated 6 months ago
• marbl / harvest
  ☆52Updated 3 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆69Updated 4 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 2 years ago
• combogenomics / medusa
  A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.
  ☆43Updated 4 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆47Updated 3 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 5 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆63Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• csmiller / EMIRGE
  EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
  ☆37Updated last year
• rrwick / Metagenomics-Index-Correction
  ☆79Updated last year
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆44Updated 3 weeks ago
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆44Updated last year
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆52Updated 9 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆70Updated 4 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• katholt / RedDog
  ☆36Updated 2 years ago
• sgearle / bugwas
  Locus and lineage tests for bacterial GWAS
  ☆29Updated 7 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 10 months ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆70Updated 5 years ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆58Updated 3 years ago