Alternatives and similar repositories for varVAMP

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

• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated this week
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆62Updated 11 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• compgenomicslab / TreeProfiler
  tree visualization for tree + annotation data
  ☆39Updated 2 months ago
• dayzerodx / counterr
  ☆31Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆38Updated 2 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 4 years ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆63Updated 2 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆53Updated 2 months ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆50Updated 7 months ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆36Updated this week
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated last month
• BeatsonLab-MicrobialGenomics / micropipe
  A pipeline for high-quality bacterial genome construction using ONT sequencing
  ☆39Updated 2 years ago
• refresh-bio / vclust
  Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
  ☆88Updated 3 months ago
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆19Updated last month
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆41Updated 4 months ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆59Updated 3 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• pauloluniyi / VGEA
  VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.
  ☆20Updated 3 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆53Updated 4 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated last year
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆43Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆29Updated 8 months ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆76Updated 2 years ago
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year