Altools

Altools detects genomic polymorphisms and structural variations from next-generation sequencing data to support genetic variation and genome structure analysis.

Key Features:

• SNP and Indel Detection: Identifies single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms using BWA, SAMtools, and VarScan.
• Structural Variation Identification: Detects structural variants including copy number variations (CNVs), presence/absence variations, and large deletions.
• Genome Segmentation for CNV Detection: Applies the dnaCopy algorithm to segment genomes based on local sequencing coverage differences.
• Breakpoint Detection: Uses paired-end read insert size information and a dual mapping strategy with BWA and BLASTn to identify large deletion breakpoints.
• Variant-Associated Gene Analysis: Links detected polymorphisms and structural variants to affected genes to support functional interpretation.

Scientific Applications:

• Population Genomics: Characterizes SNP diversity and haplotype structures across populations.
• Evolutionary Genomics: Analyzes SNPs and indels to investigate phyletic relationships and speciation patterns.
• Genome-Wide Association Studies: Identifies structural variants and polymorphisms associated with quantitative trait loci (QTLs).
• Functional Genomics: Investigates biological functions of genes affected by genomic variants.

Methodology:

Altools aligns sequencing reads to a reference genome using BWA, calls SNPs and indels with SAMtools and VarScan, segments genomes using the dnaCopy algorithm based on coverage differences to identify CNVs, and detects large deletion breakpoints using paired-end insert size information with a dual mapping strategy involving BWA and BLASTn.