Alternatives and similar repositories for harvest

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

• katholt / RedDog
  ☆36Updated 3 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆49Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 4 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 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
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• cerebis / bin3C
  Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
  ☆23Updated 3 weeks ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆29Updated 2 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• paulstothard / cgview
  CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
  ☆44Updated 11 months ago
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated last year
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆54Updated 10 months ago
• 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
• adlape95 / Spaghetti
  Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing
  ☆18Updated 11 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• metagenomics / denbi-nanopore-training
  de.NBI Nanopore Training Course
  ☆20Updated 2 weeks ago
• chjp / ANI
  Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes
  ☆19Updated 3 years ago
• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆34Updated 6 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 6 months ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆54Updated 3 years ago
• fanglab / mbin
  mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
  ☆25Updated 2 years ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 9 months ago