Nextflow Collection
Top Nextflow repositories on GitHub
UNCOMMON
⭐1.3kHP
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📦Normal
★★
rnaseq
nf-core
Nextflownextflownf-core
“RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.”
1.3k
872
1.3k
GitPedia Card512/002
UNCOMMON
⭐573HP
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📦Normal
★★
sarek
nf-core
Nextflowannotationbioinformatics
“Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing”
573
531
573
GitPedia Card765/002
UNCOMMON
⭐514HP
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📦Normal
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bactopia
bactopia
Nextflowbacterial-genomesbioconda
“A flexible pipeline for complete analysis of bacterial genomes”
514
80
514
GitPedia Card321/002
COMMON
⭐416HP
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📦Normal
★
modules
nf-core
Nextflowdsl2modules
“Repository to host tool-specific module files for the Nextflow DSL2 community!”
416
1.1k
416
GitPedia Card265/001
COMMON
⭐372HP
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📦Normal
★
patterns
nextflow-io
Nextflownextflow
“A curated collection of Nextflow implementation patterns”
372
73
372
GitPedia Card024/001
COMMON
⭐328HP
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📦Normal
★
scrnaseq
nf-core
Nextflow10x-genomics10xgenomics
“Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection”
328
219
328
GitPedia Card326/001
COMMON
⭐300HP
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📦Normal
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mag
nf-core
Nextflowannotationassembly
“Assembly and binning of metagenomes”
300
152
300
GitPedia Card634/001
COMMON
⭐248HP
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📦Normal
★
training
nextflow-io
Nextflowlearningnextflow
“Nextflow training material ”
248
313
248
GitPedia Card601/001
COMMON
⭐248HP
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📦Normal
★
ampliseq
nf-core
Nextflow16s18s
“Amplicon sequencing analysis workflow using DADA2 and QIIME2”
248
156
248
GitPedia Card800/001
COMMON
⭐240HP
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📦Normal
★
chipseq
nf-core
Nextflowchipchip-seq
“ChIP-seq peak-calling, QC and differential analysis pipeline.”
240
177
240
GitPedia Card738/001
COMMON
⭐226HP
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📦Normal
★
nanoseq
nf-core
Nextflowalignmentdemultiplexing
“Nanopore demultiplexing, QC and alignment pipeline”
226
105
226
GitPedia Card038/001
COMMON
⭐224HP
◆
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📦Normal
★
atacseq
nf-core
Nextflowatac-seqchromatin-accessibiity
“ATAC-seq peak-calling and QC analysis pipeline”
224
135
224
GitPedia Card490/001
COMMON
⭐206HP
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📦Normal
★
eager
nf-core
Nextflowadnaancient-dna-analysis
“A fully reproducible and state-of-the-art ancient DNA analysis pipeline”
206
89
206
GitPedia Card306/001
COMMON
⭐197HP
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📦Normal
★
egapx
ncbi
Nextflow
“Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation”
197
22
197
GitPedia Card943/001
COMMON
⭐193HP
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📦Normal
★
methylseq
nf-core
Nextflowbisulfite-sequencingdna-methylation
“Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair”
193
172
193
GitPedia Card076/001
COMMON
⭐192HP
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📦Normal
★
fetchngs
nf-core
Nextflowddbjdownload
“Pipeline to fetch metadata and raw FastQ files from public databases”
192
92
192
GitPedia Card339/001
COMMON
⭐188HP
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📦Normal
★
taxprofiler
nf-core
Nextflowbioinformaticsclassification
“Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data”
188
66
188
GitPedia Card755/001
COMMON
⭐174HP
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📦Normal
★
rnafusion
nf-core
Nextflowfusionfusion-genes
“RNA-seq analysis pipeline for detection of gene-fusions”
174
122
174
GitPedia Card826/001