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nf-core/proteogenomicsdb
1.0.0
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cosmic gnomad protein-databases proteogenomics
+2
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The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
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nf-core/quantms
1.2.0
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dia lfq mass-spec mass-spectrometry
+4
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Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
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nf-core/sammyseq
0.0.0-023aff4
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3d-genome chromatin dna epigenetics
+6
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Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
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nf-core/sarek
3.10.0
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annotation cancer gatk4 genomics
+7
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Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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nf-core/scnanoseq
1.3.0
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10xgenomics long-read-sequencing nanopore rna-seq
+3
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Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
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nf-core/scrnaseq
4.2.0
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10x-genomics 10xgenomics alevin bustools
+5
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Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
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nf-core/seqinspector
1.1.2
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genomics quality-control
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Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
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nf-core/spatialaxe
1.0.1
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10x-genomics atera image-processing spatial
+4
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A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
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nf-core/spatialvi
0.0.0-17d6cb0
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10x-genomics 10xgenomics image-processing microscopy
+7
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Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
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nf-core/taxprofiler
2.0.1
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classification illumina long-reads metagenomics
+7
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Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
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nf-core/tumourevo
1.0.0
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cancer-evolution cancer-genomics copy-number-variation mutational-signatures
+4
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Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
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nf-core/vipr
0.0.0-6eef3b3
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genome-assembly metagenomics variant-calling viral
+5
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Assembly and intrahost / low-frequency variant calling for viral samples
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nf-core/viralmetagenome
1.2.0
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epidemiology fastq ngs viral-metagenomics
+2
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A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
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nf-core/viralrecon
3.0.0
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amplicon artic assembly covid-19
+11
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Assembly and intrahost/low-frequency variant calling for viral samples
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