Nextflow Modules
Showing module(s) with keyword "pacbio"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bam2fastx/bam2fastq | bam2fastx bam2fastq pacbio | Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data |
| nf-core/canu | Assembly pacbio hifi nanopore | Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. |
| nf-core/hifiadapterfilt/downloaddb | pacbio hifi adapter blast database download | Downloads the pre-built PacBio adapter BLAST database from the HiFiAdapterFilt GitHub repository. The database contains two adapter sequences: NGB00972.1 (Pacific Biosciences Blunt Adapter, 45 bp) and NGB00973.1 (C2 Primer, 35 bp). This module is consumed by hifiadapterfilt/hifiadapterfilt as a prerequisite to provide the BLAST database for adapter detection. |
| nf-core/hifiadapterfilt/hifiadapterfilt | pacbio hifi adapter filtering long reads ccs | Remove adapter sequences from PacBio HiFi (CCS) reads using BLAST-based detection. Produces filtered FASTQ output, filtering statistics, BLAST hits, and a list of blocked read IDs. |
| 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/processblast | pacbio bam hifi_trimmer processblast quality control adapter removal | Run hifi_trimmer process_blast to process a BLAST search of adapter sequences against PacBio HiFi reads. Primary output is a BED describing regions to exclude, a json of summary information, and an optional hits file. |
| 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/hiphase | pacbio structural variant phasing pacbio hifi snv haplotagging | Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples |
| nf-core/isoseq3/tag | isoseq tag pacbio UMI cell_barcodes | Extract UMI and cell barcodes |
| nf-core/isoseq/refine | isoseq refine ccs pacbio polyA_tail | Remove polyA tail and artificial concatemers |
| nf-core/lima | isoseq ccs primer pacbio barcode | lima - The PacBio Barcode Demultiplexer and Primer Remover |
| nf-core/methbat/profile | methylation epigenetics pacbio | Runs methbat profile command to create methylation profiles for regions of interest from CpG metrics. |
| nf-core/miniasm | assembly pacbio nanopore | A very fast OLC-based de novo assembler for noisy long reads |
| nf-core/myloasm | assembly metagenome long-read pacbio nanopore | Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command. |
| nf-core/pbccs | ccs pacbio isoseq subreads | Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads |
| nf-core/pbcpgtools/alignedbamtocpgscores | methylation cpg pacbio | Converts aligned BAM files into CpG methylation scores |
| nf-core/pbjasmine | genomics methylation bam pacbio | Identify specific base modifications in PacBio HiFi reads by analyzing polymerase kinetic signatures |
| nf-core/pbmm2/align | align pacbio genomics |