Nextflow Modules
Showing module(s) with keyword "genomics"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/agat/spextractsequences | Process | 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 | Process | 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 | Process | 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 | Process | 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/spmergeannotations | Process | genomics gff merge combine | This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files. |
| nf-core/alignoth | Process | genomics alignment visualization pileup plotting | Creating alignment plots from bam files |
| nf-core/angsd/dosaf | Process | angsd genotype likelihood genomics | Estimate site allele frequencies from BAM files. |
| nf-core/angsd/gl | Process | angsd genotype likelihood genomics | Calculated genotype likelihoods from BAM files. |
| nf-core/angsd/realsfs | Process | angsd genotype likelihood genomics site frequency spectrum | Estimate site frequency spectrum from site allele frequencies |
| nf-core/angsd/soapsnpcalibration | Process | angsd genotype likelihood soapsnp calibration genomics | Generate ANGSD SOAPsnp genotype likelihood calibration files (counts/quality matrices) from BAM alignments. |
| nf-core/annosine | Process | genomics SINE annotation plant | Accelerating de novo SINE annotation in plant and animal genomes |
| nf-core/any2fasta | Process | 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/argnorm | Process | amr antimicrobial resistance arg antimicrobial resistance genes genomics metagenomics normalization drug categorization | Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD). |
| nf-core/artic/aligntrim | Process | artic primer trimming amplicon genomics sequencing nanopore illumina | Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files. |
| nf-core/bamclipper | Process | primer clipping genomics bam | This module is used to clip primer sequences from your alignments. |
| nf-core/bam_cnv_wisecondorx | Workflow | cnv bam bed cram plots genomics | A subworkflow for calling CNVs using WisecondorX |
| nf-core/bamreadcount | Process | BAM CRAM metrics |