Top 8 Nextflow nf-core Projects

rnaseq

14 770 9.5 Nextflow

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

5 332 9.8 Nextflow

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

Project mention: Recommendations for software or online resources | /r/bioinformatics | 2023-04-29

WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
mag

2 182 9.5 Nextflow

Assembly and binning of metagenomes
chipseq

1 169 0.0 Nextflow

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

2 159 7.7 Nextflow

ATAC-seq peak-calling and QC analysis pipeline
eager

1 125 7.8 Nextflow

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

1 77 9.7 Nextflow

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

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
hlatyping

1 51 0.0 Nextflow

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). The latest post mention was on 2023-12-09.