Ana Rita Grosso

Tools for HTS Data Pre-processing (sra toolkit, fastqc, fastX, trimGalore)

Tools for HTS Aligned Data (bedtools, samtools, UCSC tools, bedops)

Several R & BioConductor packages

R base

STAR RNA-seq alignment tool

Bismark (DNA methylation) and Bowtie2

Ensembl-VEP (Variant Effect Predictor)

Pyclone (Clonal population structure)

Tools for peak calling from ChIP-seq data (MACS2, bedtools, picard tools, samtools)

Kallisto (Transcriptome alignment and quantification)

RUBioSeq 3.8 (Variant Calling from DNA sequencing)

MutSigCV (Mutation Significance from DNA sequencing)