Nextflow Modules
Showing module(s) with keyword "long reads"
| Module | Keywords | Description |
|---|---|---|
| nf-core/catpack/addnames | taxonomic classification classification long reads mags assembly | Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins). |
| nf-core/catpack/bins | taxonomic classification classification long reads mags assembly | Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins). |
| nf-core/catpack/contigs | taxonomic classification classification long reads mags assembly | Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins). |
| nf-core/catpack/reads | taxonomic classification classification long reads mags assembly abundance taxonomic composition | Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins). |
| nf-core/catpack/summarise | taxonomic classification classification long reads mags assembly | Summarises results from CAT/BAT/RAT classification steps |
| nf-core/fastplong | trimming quality control fastq long reads | Perform adapter/quality trimming and QC on long sequencing reads (ONT, PacBio, etc.) |
| nf-core/filtlong | nanopore quality control QC filtering long reads short reads | Filtlong filters long reads based on quality measures or short read data. |
| 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/hifiasm | genome assembly haplotype resolution phasing PacBio HiFi long reads | Whole-genome assembly using PacBio HiFi reads |
| nf-core/hificnv | copy number variation cnv PacBio HiFi long reads structural variation | Copy number variant calling from PacBio HiFi reads |
| nf-core/melon | profile metagenomics melon classification long reads nanopore | Performs taxonomic profiling of long metagenomic reads against the melon database |
| nf-core/metacache/build | genomics metagenomics taxonomy short reads long reads kmer k-mer metacache build reference | Taxonomic profiling database building with MetaCache |
| nf-core/metamaps/classify | metamaps long reads metagenomics taxonomy | Strain-level metagenomic assignment |
| nf-core/metamaps/mapdirectly | metamaps long reads metagenomics taxonomy | Maps long reads to a metamaps database |
| nf-core/metamdbg/asm | assembly long reads metagenome metagenome assembler | Metagenome assembler for long-read sequences (HiFi and ONT). |
| nf-core/nanomonsv/get | structural variants nanopore cancer genome somatic structural variations long reads | Call somatic structural variants with nanomonsv get using tumor/control parse outputs and a reference genome. |
| nf-core/nanomonsv/parse | structural variants nanopore cancer genome |