Indel realignment bioinformatics tools | Next-generation sequencing analysis

Indel realignment software tools | High-throughput sequencing data analysis

Despite the fact that both Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) have been widely used in biological studies and rare disease diagnosis, limitations of these techniques on insertion and deletion (INDEL calling are still not well characterized. INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts.

ABRA / Assembly Based ReAligner

Allows next-generation sequencing read alignments. ABRA’s algorithm performs localized region assembly, contig building, alignment of assembled contigs and read realignment. The software identifies variations that are not present in the original read alignments and improves allele-frequency estimates for variations that are present. It can be used to enhance both germ-line and somatic variant detection and works with paired-end as well as single-end data.

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