Alternatives and similar repositories for SPANDx:

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

• katholt / RedDog
  ☆36Updated 3 years ago
• dsarov / ARDaP
  Comprehensive resistance detection from WGS data
  ☆19Updated 5 months ago
• marbl / harvest
  ☆52Updated 3 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆48Updated 3 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 4 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆41Updated 4 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 4 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
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆32Updated last year
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 2 weeks ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆44Updated 4 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
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 9 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆18Updated last year
• EvolBioInf / andi
  ♥ Efficient Estimation of Evolutionary Distances
  ☆46Updated last year
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆24Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• EvolBioInf / phylonium
  ♥ Fast and Accurate Estimation of Evolutionary Distances
  ☆27Updated last week