bioinformatics-fundamentals

SAM/BAM flags (0x1, 0x2, 0x4, etc.) encode read properties like paired status and alignment success; MAPQ scores quantify mapping confidence. Understanding these helps identify misaligned reads and validate assembly quality in genomics workflows.

Illumina provides short, accurate reads; PacBio HiFi delivers long reads with high accuracy; Hi-C captures chromosome interactions for 3D genome mapping. Each suits different assembly and analysis goals in genomics pipelines.

AGP files define contig and scaffold ordering. Validation involves checking coordinate continuity, gap consistency, and overlap patterns against raw assembly data to catch assembly errors early.

N50 length, coverage depth, and PHRED quality scores measure sequence completeness and accuracy. These metrics guide decisions on whether data is suitable for downstream analysis or requires resequencing.

Core formats include FASTQ/FASTA (raw reads), SAM/BAM (alignments), BED (genomic regions), VCF (variants), and AGP (scaffold definitions). Knowing their structure prevents parsing errors and data loss.

Yes. The skill covers debugging workflows and common troubleshooting patterns across assembly pipelines, helping you identify root causes in alignment, quality, or coordinate validation steps.