Nextflow Modules
Showing module(s) with keyword "FASTQ"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/rename10xsample | Process | 10x single-cell FASTQ rename Cell Ranger sample | Collects per-run Cell Ranger-style FASTQs for a sample and renames them to a consistent sample-level naming scheme, ready for downstream alignment. |
| cellgeni/sra2fastq | Process | SRA FASTQ conversion single-cell 10x public data | Converts a local SRA file to split gzipped FASTQ files using parallel-fastq-dump, producing one FASTQ per read slot ready for downstream processing. |
| nf-core/fast2q | Process | CRISPRi FASTQ genomics | A program that counts sequence occurrences in FASTQ files. |
| nf-core/fastq_find_mirna_mirdeep2 | Workflow | miRNA FASTQ FASTA Bowtie miRDeep2 | This subworkflow identifies miRNAs from FASTQ files using miRDeep2. The workflow converts FASTQ to FASTA, processes and replaces any whitespace in sequence IDs, builds a Bowtie index of the genome, and then maps reads using miRDeep2 mapper before identifying known and novel miRNAs. |
| nf-core/slimfastq | Process | FASTQ compression lossless | Fast, efficient, lossless compression of FASTQ files. |
| nf-core/spring/compress | Process | FASTQ compression lossless | Fast, efficient, lossless compression of FASTQ files. |
| nf-core/spring/decompress | Process | FASTQ decompression lossless | Fast, efficient, lossless decompression of FASTQ files. |
| nf-core/sratools/fasterqdump | Process | sequencing FASTQ dump | Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA). |