Alternatives and similar repositories for snakemake-wrappers

Users that are interested in snakemake-wrappers are comparing it to the libraries listed below

• askimed / nf-test
  Simple test framework for Nextflow pipelines
  ☆160Updated 5 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆330Updated 2 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆226Updated this week
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆175Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆268Updated last year
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆124Updated 5 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆256Updated 3 weeks ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆136Updated 10 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆224Updated 3 weeks ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆295Updated 2 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆167Updated this week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆217Updated 2 months ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆133Updated 2 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆192Updated 2 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated this week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆232Updated 4 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated 11 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆161Updated 3 weeks ago
• sequana / sequana
  Sequana: a set of Snakemake NGS pipelines
  ☆146Updated 3 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆337Updated last month
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• TransDecoder / TransDecoder
  TransDecoder source
  ☆289Updated 8 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• stevekm / nextflow-demos
  Example Nextflow pipelines and programming techniques
  ☆107Updated 3 weeks ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆311Updated 2 months ago