Contiguate draft genome assembly

Included in: viralrecon

Screen assemblies for antimicrobial resistance against multiple databases

Included in: funcscan

Screen assemblies for antimicrobial resistance against multiple databases

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

Trim sequencing adapters and collapse overlapping reads

Included in: magtaxprofiler

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

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).

Read CEL files into an ExpressionSet and generate a matrix

Included in: differentialabundance

Takes a bed12 file and converts to a GFF3 file

Included in: circrna

Converts a GFF/GTF file into a proper GTF file

Converts a GFF/GTF file into a TSV file

Included in: rnafusion

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

Included in: genomeqc