Alternatives and similar repositories for webin-cli

Users that are interested in webin-cli are comparing it to the libraries listed below

• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated this week
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 2 months ago
• nf-core / detaxizer
  A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…
  ☆21Updated last week
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆59Updated 3 months ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆57Updated last year
• broadinstitute / GATK-for-Microbes
  ☆28Updated 3 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 5 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated last year
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated last year
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆53Updated 2 months ago
• dayzerodx / counterr
  ☆31Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated 2 weeks ago
• iqbal-lab-org / clockwork
  CRyPTIC data processing pipelines
  ☆34Updated last year
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 3 weeks ago
• nextgenusfs / funannotate2
  Eukaryotic genome annotation software.
  ☆18Updated 3 weeks ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆62Updated 11 months ago
• replikation / poreCov
  SARS-CoV-2 workflow for nanopore sequence data
  ☆41Updated 3 weeks ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• compgenomicslab / TreeProfiler
  tree visualization for tree + annotation data
  ☆39Updated 2 months 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
  ☆56Updated 4 years ago
• KamilSJaron / k-mer-approaches-for-biodiversity-genomics
  k-mer learning materials
  ☆74Updated 6 months ago
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆32Updated 7 years ago