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 last year
• 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 2 weeks ago
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• fmalmeida / ngs-preprocess
  A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
  ☆34Updated last year
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆57Updated 7 months ago
• GenomiqueENS / toulligQC
  A post sequencing QC tool for Oxford Nanopore sequencers
  ☆100Updated last month
• schmeing / ReSeq
  More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original
  ☆52Updated 3 years ago
• nf-core / multiplesequencealign
  A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
  ☆35Updated last month
• telatin / seqfu2
  seqfu - Sequece Fastx Utilities
  ☆120Updated 7 months ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆53Updated 2 months ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• BioInf-Wuerzburg / proovread
  PacBio hybrid error correction through iterative short read consensus
  ☆61Updated 6 years ago
• shenwei356 / unikmer
  A versatile toolkit for k-mers with taxonomic information
  ☆80Updated this week
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆62Updated 11 months ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆75Updated last month
• beardymcjohnface / Snaketool
  Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff
  ☆51Updated last year
• nf-core / rnavar
  gatk4 RNA variant calling pipeline
  ☆52Updated last week
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆55Updated 3 weeks ago
• telatin / covtobed
  ⛰ covtobed | Convert the coverage track from a BAM file into a BED file
  ☆45Updated 2 months ago
• DrMicrobit / mira
  MIRA sequence assembler
  ☆29Updated 8 months ago
• iqbal-lab-org / clockwork
  CRyPTIC data processing pipelines
  ☆34Updated last year
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆71Updated 2 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆86Updated 2 years ago
• rpetit3 / vcf-annotator
  Add biological annotations to variants in a given VCF file.
  ☆32Updated 3 years ago
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆25Updated 2 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated 3 weeks ago
• nextflow-io / nf-schema
  Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
  ☆45Updated last week
• hsinnan75 / GSAlign
  GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
  ☆59Updated last year
• 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