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Old 11-08-2013, 02:27 AM   #1
Location: Georgia

Join Date: Mar 2013
Posts: 15
Default targeted resequencing data analysis tool


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?

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Old 11-08-2013, 03:01 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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).
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Old 11-08-2013, 08:27 AM   #3
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Yup. Align to the whole genome. Later, if you want, you can filter the .bam to only include the targeted region.
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targeted sequencing

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