nf-core/modules

Browse the 1766 modules that are currently available as part of nf-core.

abacas

Contiguate draft genome assembly

genome assembly contiguate

Included in: viralrecon

abra2

Assembly Based ReAligner for next-generation sequencing data

alignment realignment indels bam dna rna splice-junctions assembly

abricate_run

Screen assemblies for antimicrobial resistance against multiple databases

bacteria assembly antimicrobial resistance

Included in: funcscan

abricate_summary

Screen assemblies for antimicrobial resistance against multiple databases

bacteria assembly antimicrobial reistance

abritamr_run

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

bacteria fasta antibiotic resistance

abyss_abysspe

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

genome assembly genome assembler short reads de novo assembler

adapterremoval

Trim sequencing adapters and collapse overlapping reads

trimming adapters merging fastq

Included in: mag taxprofiler

adapterremovalfixprefix

Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.

adapterremoval fastq dedup

admixture

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).

ancestry population genetics admixture reference panels gwas

affy_justrma

Read CEL files into an ExpressionSet and generate a matrix

affy microarray expression matrix

Included in: differentialabundance

agat_convertbed2gff

Takes a bed12 file and converts to a GFF3 file

genome bed gff conversion

Included in: circrna

agat_convertgff2bed

Takes a GFF3 file and converts to a bed12 file

genome bed gff conversion

Included in: rnafusion