Expert tutorials, workflow guides, and deep dives into genomic file formats, NGS pipelines, variant calling, and computational biology — from the GeneConvert engineering team.
Genomic formats
supported
Genomic data
processed
Conversion
fidelity
API response
latency
Comprehensive guides covering genomic file formats, NGS analysis pipelines, and computational biology tools — maintained by our team.
File size, query speed, and compatibility tradeoffs — with actual benchmarks across 30x WGS data for each format.
From raw FASTQ to analysis-ready VCF: BQSR, HaplotypeCaller, joint genotyping, and VQSR — with real command examples and runtime estimates.
Database coverage, computational cost, output formats, and clinical annotation capabilities — a head-to-head comparison with reproducible examples.
Deep dive into quality encoding (Phred+33 vs Phred+64), interleaved FASTQ, and common parsing pitfalls with 10x paired-end data.
STAR, HISAT2, StringTie, and Kallisto each have quirks about which annotation format they accept — and when differences break your pipeline.
Everything you need to know about the VCF spec — including FILTER columns, symbolic alleles, breakend notation, and BCF binary encoding.
BED3 for simple intervals, BED6 for stranded regions, BED12 for transcript models, and why BigBed/BigWig are essential for genome browsers.
Alignment accuracy, RAM requirements, and speed benchmarks across WGS, WES, and RNA-seq data on short and long reads.
Portability, cloud integration (AWS/GCP/Azure), container support, and community ecosystem — which workflow manager fits your team's stack?
Cost modeling, spot/preemptible instance strategies, and Terra vs. AWS HealthOmics for large-scale genomic analysis across cohorts.
Practical code examples for reading, filtering, and writing SAM/BAM/VCF/FASTA files with Python — with performance comparisons and edge cases.
How to build a PON, interpret FilterMutectCalls output, and handle common artifacts — FFPE oxidative damage, strand bias, and TLOD thresholds.
Deletions, duplications, inversions, translocations, and insertions from paired-end WGS — and why ensemble callers outperform any single tool.
ACMG/AMP classification criteria, pathogenicity scoring in VEP, and integrating population frequency databases for clinical reporting.
POD5 vs. FAST5, Dorado vs. Guppy, CCS reads vs. CLR, and how Clair3/DeepVariant perform on long-read data vs. Illumina short reads.