Nextflow Modules
Showing module(s) with keyword "genome"
| Module | Keywords | Description |
|---|---|---|
| nf-core/abacas | genome assembly contiguate | Contiguate draft genome assembly |
| nf-core/abyss/abysspe | genome assembly genome assembler short reads de novo assembler | ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes. |
| nf-core/agat/convertbed2gff | genome bed gff conversion | Takes a bed12 file and converts to a GFF3 file |
| nf-core/agat/convertgff2bed | genome bed gff conversion | Takes a GFF3 file and converts to a bed12 file |
| nf-core/agat/convertspgff2gtf | genome gff gtf conversion | Converts a GFF/GTF file into a proper GTF file |
| nf-core/agat/convertspgff2tsv | genome gff gtf conversion tsv | Converts a GFF/GTF file into a TSV file |
| nf-core/agat/convertspgxf2gxf | genome gff gtf conversion | Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file |
| nf-core/agat/spstatistics | genome gff gtf statistics | Provides different type of statistics in text format from a GFF/GTF annotation file |
| nf-core/agat/sqstatbasic | genome gff gtf statistics | Provides basic statistics in text format from a GFF/GTF annotation file |
| nf-core/bbmap/align | align map fasta fastq genome reference | Align short or PacBio reads to a reference genome using BBMap |
| nf-core/bbmap/bbsplit | align map fastq genome reference | Split sequencing reads by mapping them to multiple references simultaneously |
| nf-core/bbmap/pileup | fasta genome coverage | Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file. |
| nf-core/bedtools/shift | bed shiftBed region fai sizes genome bases | Shifts each feature by specific number of bases |
| nf-core/bedtools/shuffle | bed shuffleBed region fai sizes genome bases | bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file |
| nf-core/bowtie2/align | align map fasta fastq genome reference | Align reads to a reference genome using bowtie2 |
| nf-core/bowtie2/build | build index fasta genome reference | Builds bowtie index for reference genome |
| nf-core/bowtie/align | align map fastq fasta genome reference | Align reads to a reference genome using bowtie |
| nf-core/bowtie/build | index fasta genome reference | Create bowtie index for reference genome |
| nf-core/braker3 | genome annotation braker gff gtf | Gene prediction in novel genomes using RNA-seq and protein homology information |
| nf-core/busco/busco | quality control genome transcriptome |