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nf-core repositories

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nf-core/crisprvarNextflow

[WIP] Evaluate outcomes from genome editing experiments

Last commit Jul 10, 2019

 (5 stars) (5 forks) (0 indexed issues) (0 open good first issues)
nf-core/deepmodeloptimNextflow

Stochastic Testing and Input Manipulation for Unbiased Learning Systems

Last commit Apr 30, 2026

 (31 stars) (15 forks) (6 indexed issues) (6 open good first issues)
nf-core/deepvariantNextflow

Please consider using/contributing to https://github.com/nf-core/sarek

Last commit Jul 13, 2021

 (41 stars) (26 forks) (4 indexed issues) (4 open good first issues)
nf-core/genomeqcNextflow

Compare the quality of multiple genomes, along with their annotations.

Last commit Jul 24, 2026

 (24 stars) (24 forks) (3 indexed issues) (1 open good first issue)
nf-core/hlatypingNextflow

Precision HLA typing from next-generation sequencing data

Last commit Jul 10, 2026

 (81 stars) (37 forks) (0 indexed issues) (0 open good first issues)
nf-core/kmermaidNextflow

k-mer similarity analysis pipeline

Last commit Jul 27, 2026

 (24 stars) (16 forks) (0 indexed issues) (0 open good first issues)
nf-core/pathogensurveillanceNextflow

Surveillance of pathogens using population genomics and sequencing

Last commit Jul 24, 2026

 (61 stars) (9 forks) (3 indexed issues) (1 open good first issue)
nf-core/proteinannotatorNextflow

Generation of sequence-level annotations for amino acid sequences

Last commit Jul 27, 2026

 (14 stars) (13 forks) (0 indexed issues) (0 open good first issues)
nf-core/sarekNextflow

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

Last commit Jul 30, 2026

 (589 stars) (539 forks) (6 indexed issues) (6 open good first issues)
nf-core/variantprioritizationNextflow

Bioinformatics analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine using Personal Cancer Genome Reporter (PCGR). The pipeline offers germline SNVs/INDELS intepretation and annotation using Cancer Predisposition Sequencing Reporter (CPSR).

Last commit Jun 3, 2026

 (15 stars) (12 forks) (0 indexed issues) (0 open good first issues)