Nextflow Modules
Showing module(s) with keyword "genome"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/abacas | Process | genome assembly contiguate | Contiguate draft genome assembly |
| nf-core/abyss/abysspe | Process | 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 | Process | genome bed gff conversion | Takes a bed12 file and converts to a GFF3 file |
| nf-core/agat/convertgff2bed | Process | genome bed gff conversion | Takes a GFF3 file and converts to a bed12 file |
| nf-core/agat/convertspgff2gtf | Process | genome gff gtf conversion | Converts a GFF/GTF file into a proper GTF file |
| nf-core/agat/convertspgff2tsv | Process | genome gff gtf conversion tsv | Converts a GFF/GTF file into a TSV file |
| nf-core/agat/convertspgxf2gxf | Process | genome gff gtf conversion | Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file |
| nf-core/agat/spstatistics | Process | genome gff gtf statistics | Provides different type of statistics in text format from a GFF/GTF annotation file |
| nf-core/agat/sqstatbasic | Process | genome gff gtf statistics | Provides basic statistics in text format from a GFF/GTF annotation file |
| nf-core/bam_dedup_umi | Workflow | deduplication UMI BAM genome transcriptome umicollapse umitools | BAM deduplication with UMI processing for both genome and transcriptome alignments |
| nf-core/bbmap/align | Process | align map fasta fastq genome reference | Align short or PacBio reads to a reference genome using BBMap |
| nf-core/bbmap/bbsplit | Process | align map fastq genome reference | Split sequencing reads by mapping them to multiple references simultaneously |
| nf-core/bbmap/pileup | Process | fasta genome coverage | Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file. |
| nf-core/bedtools/shift | Process | bed shiftBed region fai sizes genome bases | Shifts each feature by specific number of bases |
| nf-core/bedtools/shuffle | Process | 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 | Process | align map fasta fastq genome reference | Align reads to a reference genome using bowtie2 |
| nf-core/bowtie2/build | Process | build index fasta genome reference | Builds bowtie index for reference genome |
| nf-core/bowtie/align | Process | align map fastq fasta genome |