Alternatives and similar repositories for SPANDx

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

• 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
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• katholt / RedDog
  ☆37Updated 3 years ago
• marbl / harvest
  ☆53Updated 4 years ago
• dsarov / ARDaP
  Comprehensive resistance detection from WGS data
  ☆19Updated 2 weeks ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• EvolBioInf / phylonium
  ♥ Fast and Accurate Estimation of Evolutionary Distances
  ☆29Updated 5 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆30Updated 9 months ago
• naturalis / wgs2ncbi
  Toolkit for preparing genomes for submission to NCBI
  ☆29Updated 4 years ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆39Updated 11 months ago
• nf-core / genomeassembler
  Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
  ☆29Updated last week
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated last month
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated 2 months ago
• marbl / MetaCompass
  MetaCompass: Reference-guided Assembly of Metagenomes
  ☆38Updated last month
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆44Updated last year
• centre-for-microbiome-research / GroopM
  Metagenomic binning suite
  ☆29Updated 2 years ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 3 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• mdcao / npScarf
  ☆26Updated 5 years ago
• adlape95 / Spaghetti
  Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing
  ☆18Updated last year
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• HKU-BAL / MegaPath-Nano
  MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…
  ☆14Updated 3 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• sirselim / guppy_parameter_optimiser
  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
  ☆30Updated 3 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆66Updated 3 years ago