targeted resequencing data analysis tool

[BhariD]

Hi,

What tool would you recommend for aligning/assembling data obtained from targeted sequencing (Illumina paired-end) of a gene of interest (species is homo sapiens) from different samples?

Appreciate any suggestions or feedback?

Regards,
BD

[dpryan]

Lacking further details, I would presume that simply aligning with whatever aligner you normally use (bowtie2, bwa, novoalign, etc.) would do what you want. If this is from a capture experiment, you might want to align to the whole genome to decrease incorrect mappings (assuming that this is important for you, which I'm going to guess it is).

[swbarnes2]

Yup. Align to the whole genome. Later, if you want, you can filter the .bam to only include the targeted region.