Alternatives and similar repositories for lathe:

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

• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 4 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆52Updated 11 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• rrwick / Metagenomics-Index-Correction
  ☆81Updated last year
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 11 months ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆48Updated 8 months ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆41Updated 2 weeks ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆47Updated 2 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆33Updated last year
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆40Updated 3 years ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 2 weeks ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆40Updated 4 months ago
• rhysf / Synima
  Synteny Imager
  ☆61Updated 7 months ago
• xiaoli-dong / metaerg
  ☆41Updated 4 years ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆73Updated last year
• AuReMe / emapper2gbk
  Convert GFF, fastas, annotation table and species name into Genbank.
  ☆14Updated last week
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆60Updated 2 months ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆45Updated last week
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆63Updated 3 years ago
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆64Updated 3 months ago