NGS bioinformatics

Canine SNP Project

Bioinformatics pipeline for identifying SNPs associated with canine degenerative myelopathy from low-coverage whole-genome sequencing data.

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Background

Canine degenerative myelopathy has genetic risk factors, but NGS data needs a reproducible path from raw SRA reads to candidate SNPs and gene-level interpretation.

Canine SNP Project is a bioinformatics pipeline for investigating single-nucleotide polymorphisms associated with canine degenerative myelopathy. The source data is public low-coverage whole-genome sequencing from the Sequence Read Archive entry SRX9665373, including paired-end Illumina NovaSeq 6000 reads from a Canis lupus familiaris sample.

The page should be read as a pipeline project: obtain raw SRA reads, prepare the data, align against a reference genome, search for SNPs, and connect candidate variants back to genes that can be interpreted in the context of disease risk.

Project Workflow

Start from public sequencing data

Use SRA accession SRX9665373 and run SRR13233412 as the raw paired-end whole-genome sequencing source.

Prepare reads before variant work

Move raw reads through a preparation step so alignment and SNP search are reproducible.

Align and search for variants

Map the canine reads to a reference genome, then search for SNPs that can be investigated further.

Connect variants to genes

Translate candidate SNPs into gene-level context for canine degenerative myelopathy interpretation.

IGV Interpretation

IGV screenshots turn the alignment output into variant-level evidence.

The repository screenshots show progressively tighter views of chromosome 31. Read coverage, mismatched base colors, and read orientation help distinguish candidate SNP evidence from ordinary alignment context.

IGV screenshot showing chromosome 31 from 26,658,238 to 26,660,830 with aligned sorted BAM reads.
Broad IGV locus viewThe broad chromosome 31 window shows where the aligned read pileup sits inside the surrounding reference context. Sparse coverage is expected for low-coverage whole-genome sequencing, so the useful signal is concentrated in the local read stack rather than across the full interval.
IGV screenshot zoomed to chromosome 31 from 26,660,134 to 26,660,343 with several aligned reads and colored base mismatches.
Candidate read supportThe tighter window exposes individual reads spanning the candidate region. Colored bases within mostly green aligned reads mark mismatches or base-level differences to inspect before treating a position as a candidate SNP.
IGV screenshot zoomed to chromosome 31 from 26,660,287 to 26,660,327 with reference bases and aligned reads visible.
Base-level variant inspectionAt 40 bp resolution, the reference bases are visible above the alignments. The colored mismatches in the read track help identify exact positions that warrant downstream gene lookup and caution against overinterpreting unsupported single-read differences.