Contiguate draft genome assembly

genomeassemblycontiguate
Included in: viralrecon

Screen assemblies for antimicrobial resistance against multiple databases

bacteriaassemblyantimicrobial resistance
Included in: funcscan

Screen assemblies for antimicrobial resistance against multiple databases

bacteriaassemblyantimicrobial reistance

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

bacteriafastaantibiotic resistance

Trim sequencing adapters and collapse overlapping reads

trimmingadaptersmergingfastq
Included in: magtaxprofiler

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

adapterremovalfastqdedup

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).

ancestrypopulation geneticsadmixturereference panelsgwas

Read CEL files into an ExpressionSet and generate a matrix

affymicroarrayexpressionmatrix
Included in: differentialabundance

Takes a bed12 file and converts to a GFF3 file

genomebedgffconversion
Included in: circrna

Converts a GFF/GTF file into a proper GTF file

genomegffgtfconversion

Converts a GFF/GTF file into a TSV file

genomegffgtfconversiontsv
Included in: rnafusion

Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file

genomegffgtfconversion
Included in: genomeqc