Alternatives and similar repositories for VGEA

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

• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆34Updated last year
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated last week
• Psy-Fer / interARTIC
  InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
  ☆31Updated last year
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆30Updated 2 months ago
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆59Updated 2 months ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆44Updated last month
• Stephane-S / Simplot_PlusPlus
  ☆39Updated 2 years ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆63Updated 5 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆44Updated 3 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
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last month
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆46Updated 2 years ago
• chmccarthy / Pangloss
  Pangenome analysis of eukaryotes.
  ☆20Updated 5 years ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆65Updated 6 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 4 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆42Updated last month
• marbl / MetaCompass
  MetaCompass: Reference-guided Assembly of Metagenomes
  ☆40Updated 3 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆43Updated 5 years ago
• fanglab / mbin
  mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
  ☆25Updated 2 years ago
• chiulab / SURPI-plus-dist
  This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…
  ☆42Updated 6 years ago
• FredHutch / gig-map
  Build a map of genes present across a set of microbial genomes
  ☆18Updated this week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• metagenomics / denbi-nanopore-training
  de.NBI Nanopore Training Course
  ☆20Updated 5 months ago
• B-UMMI / long-read-catalog
  catalog for long-read sequencing tools
  ☆32Updated 2 years ago
• zibraproject / zika-pipeline
  The Zika bioinformatics pipeline
  ☆36Updated 5 years ago