Nextflow nextflow

Open-source Nextflow projects categorized as nextflow
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Topics: nf-core Workflow Pipeline Bioinformatics Genomics
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Top 10 Nextflow nextflow Projects

  • rnaseq

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    • Project mention: R pipelines for bulk RNA-seq analyses | /r/bioinformatics | 2023-12-09

  • sarek

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

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  • patterns

    A curated collection of Nextflow implementation patterns (by nextflow-io)

  • mag

    Assembly and binning of metagenomes

  • chipseq

    ChIP-seq peak-calling, QC and differential analysis pipeline.

  • atacseq

    ATAC-seq peak-calling and QC analysis pipeline

  • eager

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

  • SaaSHub

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  • configs

    Config files used to define parameters specific to compute environments at different Institutions (by nf-core)

  • rnaseq-nf

    A proof of concept of RNAseq pipeline

  • hlatyping

    Precision HLA typing from next-generation sequencing data

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Nextflow nextflow related posts

  • Point of using Hisat2 build to index reference genomes when working with known genomes mouse/human?

    1 project | /r/bioinformatics | 29 May 2023

  • I used featureCounts to quantify RNA-seq reads and got a low successful alignment percentage. Is this a problem?

    1 project | /r/bioinformatics | 18 May 2023

  • Recommendations for software or online resources

    1 project | /r/bioinformatics | 29 Apr 2023

  • How to know where to align if I have RNAseq data??

    1 project | /r/bioinformatics | 9 Mar 2023

  • Semi Budget-Friendly High-Thread Count Options?

    1 project | /r/HomeServer | 13 Feb 2023

  • Best somatic variant callers?

    1 project | /r/bioinformatics | 9 Feb 2023

  • How to get NGS programming experience?

    1 project | /r/bioinformatics | 31 Jan 2023
  • A note from our sponsor - InfluxDB
    www.influxdata.com | 20 May 2024
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Index

What are some of the best open-source nextflow projects in Nextflow? This list will help you:

Project Stars
1 rnaseq 790
2 sarek 340
3 patterns 317
4 mag 182
5 chipseq 173
6 atacseq 161
7 eager 124
8 configs 77
9 rnaseq-nf 63
10 hlatyping 52

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