Alternatives and similar repositories for pipelines

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

• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆57Updated 4 months ago
• DrMicrobit / mira
  MIRA sequence assembler
  ☆29Updated 5 months ago
• Golob-Minot / geneshot
  ☆28Updated 11 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…
  ☆20Updated this week
• nextflow-io / nf-validation
  Params validation plugin for Nextflow pipelines
  ☆48Updated 9 months ago
• fmalmeida / ngs-preprocess
  A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
  ☆34Updated 11 months ago
• cpockrandt / PhyloCSFpp
  PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…
  ☆31Updated 3 years ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆59Updated 8 months ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆74Updated 2 weeks ago
• replikation / poreCov
  SARS-CoV-2 workflow for nanopore sequence data
  ☆40Updated 3 weeks ago
• nextflow-io / nf-schema
  Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
  ☆41Updated 3 weeks ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 11 months ago
• broadinstitute / GATK-for-Microbes
  ☆27Updated 3 years ago
• IARCbioinfo / alignment-nf
  Whole Exome/Whole Genome Sequencing alignment pipeline
  ☆28Updated 8 months ago
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆52Updated this week
• Psy-Fer / interARTIC
  InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
  ☆31Updated last year
• epi2me-labs / wf-alignment
  ☆28Updated 3 weeks 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
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆26Updated last month
• TimoLassmann / samstat
  SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.
  ☆24Updated last year
• theiagen / public_health_bacterial_genomics
  ☆26Updated last year
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated last month
• Gabaldonlab / perSVade
  perSVade: personalized Structural Variation detection
  ☆39Updated 3 months ago
• jonathancrabtree / Circleator
  Flexible circular visualization of genome-associated data with BioPerl and SVG.
  ☆47Updated 5 years ago
• OpenGene / UniqueKMER
  Generate unique KMERs for every contig in a FASTA file
  ☆48Updated 2 years ago
• WallauBioinfo / ViralFlow
  Workflow for viral analysis guided by reference
  ☆12Updated last month
• B-UMMI / long-read-catalog
  catalog for long-read sequencing tools
  ☆32Updated 2 years ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 9 months ago
• metagenomics / denbi-nanopore-training
  de.NBI Nanopore Training Course
  ☆20Updated 2 years ago
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆37Updated 5 years ago