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nf-core/bamtofastq
2.2.1
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bamtofastq conversion cramtofastq
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Converts bam or cram files to fastq format and does quality control.
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nf-core/demultiplex
1.8.0
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bases2fastq bcl2fastq demultiplexing elementbiosciences
+1
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Demultiplexing pipeline for sequencing data
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nf-core/detaxizer
1.3.0
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de-identification decontamination edna fastq
+10
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A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
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nf-core/diseasemodulediscovery
0.0.0-a20b5b0
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active-modules complex-diseases disease-mechanisms disease-modules
+9
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A pipeline for network-based disease module identification.
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nf-core/drugresponseeval
1.3.0
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cell-lines cross-validation deep-learning drug-response
+9
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Pipeline for testing drug response prediction models in a statistically and biologically sound way.
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nf-core/dualrnaseq
1.0.0
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dualrna-seq host-pathogen quantification readmapping
+1
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Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
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nf-core/fastqrepair
1.1.1
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corruption data-cleaning data-recovery fastq
+6
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A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
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nf-core/fastquorum
2.0.0
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consensus umi umis unique-molecular-identifier
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Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
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nf-core/fetchngs
1.13.0
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ddbj download ena fastq
+3
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Pipeline to fetch metadata and raw FastQ files from public databases
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nf-core/funcscan
4.0.0
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amp amr antibiotic-resistance antimicrobial-peptides
+11
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(Meta-)genome screening for functional and natural product gene sequences
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nf-core/genomeskim
0.0.0-ba97621
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chloroplast-genome genome genome-skimming mitochondrial-genomes
+1
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QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
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nf-core/hgtseq
1.1.0
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bwa-mem bwa-mem2 fastqc genomics-visualization
+9
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A pipeline to investigate horizontal gene transfer from NGS data
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nf-core/lsmquant
1.0.3
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3dunet image-analysis image-processing light-sheet-microcopy
+2
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A pipeline for processing and analysis of light-sheet microscopy images.
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nf-core/marsseq
1.0.3
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facs-sorting mars-seq single-cell single-cell-rna-seq
+2
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MARS-seq v2 pre-processing pipeline with velocity
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nf-core/mcmicro
2.0.0
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bioformats image-analysis image-processing microscopy
+8
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An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
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nf-core/methylseq
4.2.0
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bisulfite-sequencing dna-methylation em-seq epigenome
+6
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Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
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nf-core/nanostring
1.3.3
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nanostring nanostringnorm
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An analysis pipeline for Nanostring nCounter expression data.
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nf-core/neutronstar
1.0.0
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10x-genomics 10xgenomics denovo-assembly genome-assembly
+2
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De novo assembly pipeline for 10X linked-reads using Supernova
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nf-core/pairgenomealign
3.0.4
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comparative-genomics dot-plot genomics last
+3
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Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
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nf-core/plasmodiumdrugres
0.0.0-a333327
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drug-resistance frequency-estimation genomics haplotypes
+6
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Pipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. Translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.
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