Alignment of reads obtained from HaloPlex HS target-enriched sequencing
Hello everyone,
I have reads that are obtained from HaloPlex HS target-enriched sequencing (Illumina MiSeq platform).
As per my understanding, molecular barcodes are used to generate consensus sequences during alignment. https://www.agilent.com/cs/library/w...991-7421EN.pdf
I don't want to use Sure Call aligner for aligning my reads.
I saw various post in which many people are using BWA aligner.
But how BWA aligner should be used so that it will include the molecular barcoding analysis, and what parameters should be used and why ?
I have reads that are obtained from HaloPlex HS target-enriched sequencing (Illumina MiSeq platform).
As per my understanding, molecular barcodes are used to generate consensus sequences during alignment. https://www.agilent.com/cs/library/w...991-7421EN.pdf
I don't want to use Sure Call aligner for aligning my reads.
I saw various post in which many people are using BWA aligner.
But how BWA aligner should be used so that it will include the molecular barcoding analysis, and what parameters should be used and why ?