New Technologies

Question 1

NGS software processing stages and tools.

Answer 1

1) . Quality control (e.g. FASTQ) - Generates FASTQ files.
2) . Mapping (e.g. BWA, stampy, Bowtie) - BAM files.
3) . Visualisation of BAM aligned files (IGV viewer).
4) . Variant calling (e.g. GATK, SAMtools, Platypus) - VCF files / tab file exported into database.
5) . Downstream analysis (e.g. SIFT, ANNOVAR) -

Question 2

NGS data analysis alternative GUI tools.

Answer 2

• Galaxy.
• Alamut interactive software.
• Miseq Avadis software.

Question 3

Alternative NGS assays.

Answer 3

• Re-sequencing assays: genes, WES, WGS.
• Methylation assays: MeDIP, bisulphite sequencing.
• Chip-seq assays - transcription factors / elements.
• RNA-seq - RNA expression.

Question 4

What are the alternatives to resequencing NGS type tech?

Answer 4

• Variant genotype or sequencing arrays.
• Cheaper.
• Custom built for rare and low frequency variants.
• Use on large numbers.
• Easier to analyse than NGS.