Nextflow Modules
Showing module(s) with keyword "fasta"
| Module | Keywords | Description |
|---|---|---|
| nf-core/abritamr/run | bacteria fasta antibiotic resistance | A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes |
| nf-core/agat/spextractsequences | genomics gff extract fasta sequence feature | This script extracts sequences in fasta format according to features described in a gff file. |
| nf-core/agrvate | fasta virulence Staphylococcus aureus | Rapid identification of Staphylococcus aureus agr locus type and agr operon variants |
| nf-core/amrfinderplus/run | bacteria fasta antibiotic resistance | Identify antimicrobial resistance in gene or protein sequences |
| nf-core/amrfinderplus/update | bacteria fasta antibiotic resistance | Identify antimicrobial resistance in gene or protein sequences |
| nf-core/any2fasta | fasta conversion sequences format genomics | Convert various sequence formats (GenBank, GFF, FASTQ, FASTA, CLUSTAL, Stockholm, GFA) to FASTA format. Input files may be gzip, bzip2, zip, or zstd compressed. |
| nf-core/art/illumina | fastq fasta illumina simulate | Simulation tool to generate synthetic Illumina next-generation sequencing reads |
| nf-core/bakta/bakta | annotation fasta bacteria | Annotation of bacterial genomes (isolates, MAGs) and plasmids |
| nf-core/bakta/baktadbdownload | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/bamtools/convert | 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/bbmap/align | align map fasta fastq genome reference | Align short or PacBio reads to a reference genome using BBMap |
| nf-core/bbmap/filterbyname | fastq fasta filter | Filter out sequences by sequence header name(s) |
| nf-core/bbmap/index | map index fasta | Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode. |
| nf-core/bbmap/pileup | fasta genome coverage | Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file. |
| nf-core/bbmap/sendsketch | taxonomy classification sketch query fastq fasta | Compares query sketches to reference sketches hosted on a remote server via the Internet. |
| nf-core/bedtools/getfasta | bed fasta getfasta | extract sequences in a FASTA file based on intervals defined in a feature file. |
| nf-core/bedtools/maskfasta | bed fasta maskfasta | masks sequences in a FASTA file based on intervals defined in a feature file. |
| nf-core/bioawk | bioawk fastq fasta sam file manipulation awk | Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats. |
| nf-core/biscuit/index | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index reference fasta | Indexes a reference genome for use with Biscuit |
| nf-core/bismark/genomepreparation | bismark 3-letter |