Giters
nf-core

nf-core

Organization data from Github https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Home Page:http://nf-co.re

GitHub:@nf-core

Twitter:@nf_core

nf-core's repositories

sarek

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

Language:NextflowLicense:MITStargazers:500Issues:149Issues:819

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

Language:NextflowLicense:MITStargazers:385Issues:207Issues:2456

tools

Python package with helper tools for the nf-core community.

Language:PythonLicense:MITStargazers:278Issues:162Issues:1260

mag

Assembly and binning of metagenomes

Language:NextflowLicense:MITStargazers:250Issues:170Issues:372

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Language:NextflowLicense:MITStargazers:225Issues:163Issues:394

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Language:NextflowLicense:MITStargazers:179Issues:166Issues:177

taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Language:NextflowLicense:MITStargazers:168Issues:165Issues:238

test-datasets

Test data to be used for automated testing with the nf-core pipelines

License:MITStargazers:142Issues:157Issues:59

configs

Config files used to define parameters specific to compute environments at different Institutions

Language:NextflowLicense:MITStargazers:104Issues:172Issues:54

website

Code and files for the main nf-core website.

Language:MDXLicense:MITStargazers:81Issues:164Issues:495

rnavar

gatk4 RNA variant calling pipeline

Language:NextflowLicense:MITStargazers:55Issues:122Issues:83

epitopeprediction

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

Language:NextflowLicense:MITStargazers:48Issues:157Issues:86

hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Language:NextflowLicense:MITStargazers:26Issues:176Issues:4

phaseimpute

A bioinformatics pipeline to phase and impute genetic data

Language:NextflowLicense:MITStargazers:25Issues:160Issues:81

detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

Language:NextflowLicense:MITStargazers:22Issues:184Issues:10

genomeqc

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

Language:NextflowLicense:MITStargazers:18Issues:16Issues:79

methylong

Extract methylation calls from long reads (ONT/ PacBio)

Language:NextflowLicense:MITStargazers:16Issues:2Issues:0

seqinspector

QC pipeline to inspect your sequences

Language:NextflowLicense:MITStargazers:14Issues:172Issues:37

molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

Language:NextflowLicense:MITStargazers:13Issues:167Issues:48

pixelator

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

Language:NextflowLicense:MITStargazers:12Issues:174Issues:25

createpanelrefs

Generate Panel of Normals, models or other similar references from lots of samples

Language:NextflowLicense:MITStargazers:11Issues:157Issues:13

rnadnavar

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

Language:NextflowLicense:MITStargazers:11Issues:158Issues:8

sopa

Nextflow version of Sopa - spatial omics pipeline and analysis

Language:NextflowLicense:MITStargazers:11Issues:0Issues:0

meerpipe

nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis

Language:NextflowLicense:MITStargazers:10Issues:196Issues:2

logos

Host nf-core logos and templates for making new logos

License:MITStargazers:7Issues:191Issues:5

lsmquant

A pipeline for processing and analysis of light-sheet microscopy images.

Language:NextflowLicense:MITStargazers:5Issues:0Issues:0

sammyseq

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

Language:NextflowLicense:MITStargazers:5Issues:171Issues:36

ops

Different *Ops related scripts for the nf-core org.

Language:PythonStargazers:3Issues:7Issues:88

panoramaseq

a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays

Language:HTMLLicense:MITStargazers:0Issues:0Issues:0

rarevariantburden

Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.

Language:NextflowLicense:MITStargazers:0Issues:0Issues:0