Alternatives and similar repositories for pipelines

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

• Golob-Minot / geneshot
  ☆29Updated last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆57Updated 11 months ago
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆57Updated 6 months ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆48Updated 2 years ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆76Updated last week
• salzberg-lab / Balrog
  Bacterial Annotation by Learned Representation of Genes
  ☆57Updated 4 years ago
• PedroMTQ / mantis
  A package to annotate protein sequences
  ☆60Updated 5 months ago
• DrMicrobit / mira
  MIRA sequence assembler
  ☆29Updated 7 months ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 3 months ago
• telatin / seqfu2
  seqfu - Sequece Fastx Utilities
  ☆119Updated 6 months ago
• iqbal-lab-org / clockwork
  CRyPTIC data processing pipelines
  ☆34Updated last year
• replikation / poreCov
  SARS-CoV-2 workflow for nanopore sequence data
  ☆41Updated this week
• GenomiqueENS / toulligQC
  A post sequencing QC tool for Oxford Nanopore sequencers
  ☆99Updated 2 weeks ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆61Updated 11 months ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆50Updated last month
• fmalmeida / ngs-preprocess
  A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
  ☆34Updated last year
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• schmeing / ReSeq
  More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original
  ☆52Updated 2 years ago
• 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
• broadinstitute / viral-pipelines
  viral-ngs: complete pipelines
  ☆65Updated last week
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆56Updated 4 years ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆58Updated 4 months ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆62Updated 11 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆54Updated last month
• NBISweden / aMeta
  Ancient microbiome snakemake workflow
  ☆26Updated 3 months ago
• bcgsc / ntJoin
  🔗Genome assembly scaffolder using minimizer graphs
  ☆84Updated 10 months ago
• eclarke / swga
  Select primer sets for selective whole genome amplification (SWGA)
  ☆32Updated 6 years ago
• MHH-RCUG / Wochenende
  Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
  ☆37Updated 2 years ago