Nextflow Modules
Showing module(s) with keyword "trimming"
| Module | Keywords | Description |
|---|---|---|
| nf-core/adapterremoval | trimming adapters merging fastq | Trim sequencing adapters and collapse overlapping reads |
| nf-core/bbmap/bbduk | trimming adapter trimming quality trimming fastq | Adapter and quality trimming of sequencing reads |
| nf-core/chelae/trim | trimming quality control fastq adapter umi | Adapter and quality trimming of short-read FASTQ data using chelae. |
| nf-core/chopper | filter trimming fastq nanopore qc | Filter and trim long read data. |
| nf-core/chromap/chromap | chromap alignment map fastq bam sam hi-c atac-seq chip-seq trimming duplicate removal | Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap. |
| nf-core/clipkit | alignment trimming phylogeny | A multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. |
| nf-core/cutadapt | adapter primers poly-A tails trimming fastq | Removes adapter sequences from sequencing reads |
| nf-core/dragen/germline | check fingerprint copy number variation fastqc genomics germline quality control repeat expansion detection structural variation trimming variable number tandem repeat detection variant annotation variant calling variant deduplication | The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN Platform. The pipeline includes highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions and targeted calls. |
| nf-core/faqcs | trimming quality control fastq faqcs | Perform adapter and quality trimming on sequencing reads with reporting |
| nf-core/fastp | trimming quality control fastq | Perform adapter/quality trimming on sequencing reads |
| nf-core/fastplong | trimming quality control fastq long reads | Perform adapter/quality trimming and QC on long sequencing reads (ONT, PacBio, etc.) |
| nf-core/hifitrimmer/filterbam | pacbio bam fasta hifi_trimmer filtering trimming quality control adapter removal | Run hifi_trimmer filter_bam to filter and trim adapter hits from PacBio HiFi reads (BAM/FASTA/FASTQ) using BLAST against adapter sequences. Primary output is filtered FASTA/FASTQ. |
| nf-core/hifitrimmer/trim | pacbio bam fasta fastq hifi_trimmer filtering trimming quality control adapter removal | Run hifi-trimmer trim to filter and trim adapter-hit regions from PacBio HiFi reads. Supports BAM/CRAM/FASTA/FASTQ input and emits gzip-compressed FASTA (default) or FASTQ, or SAM, BAM, or CRAM according to the selected output format. |
| nf-core/ivar/trim | amplicon sequencing trimming fasta | Trim primer sequences rom a BAM file with iVar |
| nf-core/leehom | ancient DNA adapter removal clipping trimming merging collapsing preprocessing bayesian | Bayesian reconstruction of ancient DNA fragments |
| nf-core/pychopper | sort trimming nanopore | Identify, orient and trim nanopore cDNA reads |