Alternatives and similar repositories for public-health-pipeline-best-practices

Users that are interested in public-health-pipeline-best-practices are comparing it to the libraries listed below

• artic-network / fieldbioinformatics
  The ARTIC fieldbioinformatics pipeline
  ☆125Updated 3 weeks ago
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆104Updated 4 years ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆162Updated last month
• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆91Updated 2 years ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆95Updated this week
• ngs-fzb / MTBseq_source
  MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…
  ☆46Updated 2 months ago
• CSB5 / OPERA-MS
  OPERA-MS - Hybrid Metagenomic Assembler
  ☆100Updated last year
• SorenKarst / longread_umi
  ☆79Updated 5 years ago
• OpenGene / fastplong
  Ultra-fast preprocessing and quality control for long-read sequencing data
  ☆194Updated 2 months ago
• asl / BandageNG
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆150Updated last week
• nanoporetech / read_until_api
  Read Until client library for Nanopore Sequencing
  ☆106Updated last year
• medvedevgroup / SibeliaZ
  A fast whole-genome aligner based on de Bruijn graphs
  ☆153Updated 4 months ago
• sanger-pathogens / assembly-stats
  Get assembly statistics from FASTA and FASTQ files
  ☆123Updated 2 years ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆39Updated last month
• thegenemyers / FASTGA
  Pairwise whole genome aligner
  ☆201Updated this week
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆149Updated 7 months ago
• ksahlin / strobealign
  Aligns short reads using dynamic seed size with strobemers
  ☆181Updated this week
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆141Updated 2 months ago
• wdecoster / chopper
  ☆218Updated last week
• GaetanBenoitDev / metaMDBG
  MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
  ☆179Updated last month
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆52Updated 11 months ago
• rrwick / Perfect-bacterial-genome-tutorial
  ☆148Updated last year
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆114Updated 6 months ago
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆146Updated last month
• nanoporetech / qcat
  qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
  ☆81Updated 4 years ago
• jtlovell / GENESPACE
  ☆219Updated 9 months ago
• nanoporetech / ont-assembly-polish
  ONT assembly and Illumina polishing pipeline
  ☆89Updated 4 years ago
• PacificBiosciences / pb-metagenomics-tools
  Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
  ☆195Updated last month
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆197Updated 2 months ago
• eblerjana / pangenie
  Pangenome-based genome inference
  ☆149Updated 3 months ago