Nextflow Registry | Nextflow Pipelines

Nextflow Pipelines

Nextflow pipelines hosted in Git repositories. Each published release records the Git revision it runs and the launch configuration it ships with.

8 pipeline(s) matching "fastq".

Pipeline	Keywords	Description
nf-core/bamtofastq 2.2.1	bamtofastq conversion cramtofastq	Converts bam or cram files to fastq format and does quality control.
nf-core/demultiplex 1.8.0	bases2fastq bcl2fastq demultiplexing elementbiosciences +1	Demultiplexing pipeline for sequencing data
nf-core/detaxizer 1.3.0	de-identification decontamination edna fastq +10	A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
nf-core/fastqrepair 1.1.1	corruption data-cleaning data-recovery fastq +6	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
nf-core/fastquorum 2.0.0	consensus umi umis unique-molecular-identifier	Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
nf-core/fetchngs 1.13.0	ddbj download ena fastq +3	Pipeline to fetch metadata and raw FastQ files from public databases
nf-core/hgtseq 1.1.0	bwa-mem bwa-mem2 fastqc genomics-visualization +9	A pipeline to investigate horizontal gene transfer from NGS data
nf-core/viralmetagenome 1.2.0	epidemiology fastq ngs viral-metagenomics +2	A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.