Nextflow Modules
Showing module(s) with keyword "fastq"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/adapterremoval | Process | trimming adapters merging fastq | Trim sequencing adapters and collapse overlapping reads |
| nf-core/adapterremovalfixprefix | Process | adapterremoval fastq dedup | Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup. |
| nf-core/ariba/getref | Process | fastq assembly resistance virulence | Download and prepare database for Ariba analysis |
| nf-core/ariba/run | Process | fastq assembly resistance virulence | Query input FASTQs against Ariba formatted databases |
| nf-core/art/illumina | Process | fastq fasta illumina simulate | Simulation tool to generate synthetic Illumina next-generation sequencing reads |
| nf-core/bamtofastq10x | Process | bam convert fastq 10x | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis |
| nf-core/bamtools/convert | Process | bamtools bamtools/convert bam convert bed fasta fastq json pileup sam yaml | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bases2fastq | Process | demultiplex element fastq | Demultiplex Element Biosciences bases files |
| nf-core/bbmap/align | Process | align map fasta fastq genome reference | Align short or PacBio reads to a reference genome using BBMap |
| nf-core/bbmap/bbduk | Process | trimming adapter trimming quality trimming fastq | Adapter and quality trimming of sequencing reads |
| nf-core/bbmap/bbmerge | Process | paired reads merging fastq overlap-based merging | Merging overlapping paired reads into a single read. |
| nf-core/bbmap/bbsplit | Process | align map fastq genome reference | Split sequencing reads by mapping them to multiple references simultaneously |
| nf-core/bbmap/clumpify | Process | clumping fastqs smaller fastqs deduping fastq | Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates |
| nf-core/bbmap/filterbyname | Process | fastq fasta filter | Filter out sequences by sequence header name(s) |
| nf-core/bbmap/repair | Process | paired reads re-pairing fastq preprocessing | Re-pairs reads that became disordered or had some mates eliminated. |
| nf-core/bbmap/sendsketch | Process | taxonomy classification sketch query fastq fasta | Compares query sketches to reference sketches hosted on a remote server via the Internet. |
| nf-core/bcl2fastq | Process | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/bclconvert | Process | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/bcl_demultiplex | Workflow | bcl bclconvert bcl2fastq demultiplex fastq |