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/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/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 | Alignment with PacBio's minimap2 frontend |
| nf-core/pbsv/call | variant pacbio genomics | pbsv/call - PacBio structural variant (SV) calling and analysis tools |
| nf-core/pbsv/discover | variant pacbio structural | pbsv - PacBio structural variant (SV) signature discovery tool |
| nf-core/pbtk/bam2fastq | convert bam genomics pacbio | converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq |
| nf-core/pbtk/pbindex | genomics bam index pacbio | Minimalistic tool which creates an index file that enables random access into PacBio BAM files |
| nf-core/pbtk/pbmerge | pbtk pbmerge genomics pacbio bam | Simple tool which merges several PacBio BAM files together |