Nextflow Modules
Showing 2,049 module(s)
| Module | Keywords | Description |
|---|---|---|
| nf-core/abra2 | alignment realignment indels bam dna rna splice-junctions assembly | Assembly Based ReAligner for next-generation sequencing data |
| nf-core/abricate/run | bacteria assembly antimicrobial resistance | Screen assemblies for antimicrobial resistance against multiple databases |
| nf-core/abricate/summary | bacteria assembly antimicrobial reistance | Screen assemblies for antimicrobial resistance against multiple databases |
| 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/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/adapterremoval | trimming adapters merging fastq | Trim sequencing adapters and collapse overlapping reads |
| nf-core/adapterremovalfixprefix | adapterremoval fastq dedup | Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup. |
| nf-core/admixture | ancestry population genetics admixture reference panels gwas | ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). |
| nf-core/affy/justrma | affy microarray expression matrix | Read CEL files into an ExpressionSet and generate a matrix |
| 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/spaddintrons | gtf gff introns | Add intron features to gtf/gff file without intron features. |
| 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/agat/spfilterbyorfsize | genomics GFF/GTF filter annotation | The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test. |
| nf-core/agat/spfilterfeaturefromkilllist | genomics gff remove feature | The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will automatically remove this feature too. |
| nf-core/agat/spflagshortintrons | genomics gtf gff intron short annotation | The script flags the short introns with the attribute <pseudo>. Is is usefull to avoid ERROR when submiting the data to EBI. (Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy) |
| nf-core/agat/spkeeplongestisoform | gff gtf filter isoform gene longest agat | Filters GFF records to keep only the longest isoform per gene |
Showing 21-40 of 2,049 modules