Bioinformatics analysis service
DNA sequencing reads become filtered SNV and indel calls under GATK Best Practices [1], with optional CNV/SV modules, pinned pipelines, figures, and a Methods draft.
| Category | Details |
|---|---|
| Data types supported | Illumina short-read paired-end FASTQ or BAM; MGI DNBSEQ-T7 / G400 / G99 when scoped at kickoff; Element Biosciences AVITI and Ultima UG100 when scoped at kickoff; PacBio and Oxford Nanopore long-read FASTQ for the long-read spoke; pre-aligned BAM or gVCF for variant-calling-only projects |
| Reference builds or standards used | Human GRCh38 primary with GATK resource bundle 4.6 [2]; GRCh38 alternate loci per functional-equivalence standards [3]; legacy GRCh37/hg19; mouse GRCm39; custom references scoped at kickoff |
| Primary tools (with versions) | BWA-MEM2 2.2.1; GATK 4.6.0.0; Picard 3.2.0; samtools/bcftools 1.21; mosdepth 0.3.3; Ensembl VEP 112; Manta 1.6.0; DELLY 1.2.6; minimap2 2.28; Clair3 1.0.9; fastp 0.23.4; FastQC 0.12.1; MultiQC 1.25; DeepVariant 1.8.0 optional |
| Typical turnaround range | 2-4 weeks (single-sample germline); 4-8 weeks (multi-sample cohort with joint genotyping and VQSR), confirmed at kickoff |
| Deliverable formats | .bam, .g.vcf.gz, filtered .vcf.gz, annotation .tsv, CNV/SV call tables; PDF/SVG figures; HTML QC report; commented bash/R/Python scripts; Methods draft |
| Regulatory/reproducibility standards followed | GATK Best Practices [1]; functional-equivalence alignment standards [3]; MD5 checksum validation; version-pinned software with documented parameters; clinical validation guidance where applicable [4, 5] |
Genomics studies an organism's complete DNA sequence and the computational analysis used to detect variation against a reference genome. A single-nucleotide variant (SNV) is a one-base change; an indel is a short insertion or deletion; a copy-number variant (CNV) is a gain or loss of genomic segments; and a structural variant (SV) is a larger rearrangement such as an inversion or translocation. Typical questions include which DNA sequence changes relate to disease risk, drug response, or evolutionary divergence. The NIH All of Us Research Program released 245,350+ whole-genome sequences to researchers by 2023, with planned releases exceeding 400,000 WGS [10].
Genomics analysis identifies inherited and somatic DNA changes linked to disease mechanism, treatment response, and population genetic architecture. Applications include rare undiagnosed disorders, cancer driver catalogs, and cohort-scale association studies [4, 11]. The examples below pair research questions with published results.
Clinical WGS validation guidelines emphasize detecting noncoding variants and structural changes that WES may miss [4].
Kinnersley et al. [11] analyzed 10,478 cancer WGS profiles across 35 tumor types, identifying 330 candidate driver genes; approximately 55% of patients harbor at least one clinically relevant mutation.
Light et al. [12] reported near-ubiquitous early TP53 LOH with gain of the mutant allele years before tumor diagnosis in Li-Fraumeni syndrome WGS data.
Gabrielaite et al. [13] benchmarked 11 CNV callers on matched WES and WGS data and suggested combining GATK gCNV, Lumpy, DELLY, and cn.MOPS, since no single caller in that comparison captured all CNV classes reliably.
Regier et al. [3] defined functional-equivalence standards, including BWA-MEM alignment, GRCh38 with alternate loci, and CRAM compression, that reduce cross-center call discordance.
| Service | Description | Primary tools |
|---|---|---|
| Whole-genome sequencing | Genome-wide germline SNV and indel discovery from raw FASTQs with callable-region QC | BWA-MEM2, GATK HaplotypeCaller, Ensembl VEP |
| Whole-exome sequencing | Targeted coding-region variant calling from capture-enriched libraries at lower sequencing cost than WGS | BWA-MEM2, GATK, VEP; capture-aware depth QC |
| Variant calling | SNV/indel calling, joint genotyping, and filter tuning when alignment is already complete | GATK HaplotypeCaller, DeepVariant, bcftools |
| CNV and structural variation | Genome-wide copy-number and structural variant detection from WGS or WES alignments | GATK gCNV, Manta, DELLY; CNVkit when scoped |
| Long-read DNA sequencing | Phased variants and structural events from PacBio or Oxford Nanopore reads | minimap2, Clair3; long-read SV callers when scoped |
Genomics projects include filtered variant files, coverage QC tables, annotated figures, version-pinned scripts, and a Methods draft. Extra outputs can be added at kickoff. Standard deliverables include:
Verify FASTQ or BAM integrity (MD5 checksums), read layout, read groups, and experimental design; record sample_manifest.csv and flag sub-threshold yield.
Tools used: md5sum; custom validation scripts
FastQC 0.12.1 and fastp 0.23.4 assess and trim reads; flag low Q30 or high-adapter libraries before alignment.
BWA-MEM2 2.2.1 aligns short reads to GRCh38; minimap2 2.28 on the long-read spoke; samtools 1.21 indexes coordinate-sorted BAMs.
Picard 3.2.0 MarkDuplicates and GATK 4.6.0.0 BaseRecalibrator / ApplyBQSR using the GATK resource bundle.
mosdepth 0.3.3 and Picard CollectWgsMetrics or CollectHsMetrics report mean coverage and breadth at agreed thresholds [4].
GATK 4.6.0.0 HaplotypeCaller in gVCF mode; GenomicsDBImport and GenotypeGVCFs for cohorts; DeepVariant 1.8.0 optional [8].
GATK gCNV, Manta 1.6.0, DELLY 1.2.6, and CNVkit when scoped; Gabrielaite et al. [13] suggested combining multiple CNV methods.
Ensembl VEP 112 annotation; GATK VQSR or hard filters [2]; bcftools 1.21; MultiQC 1.25; final scripts, README, Methods draft, and figures.
Core stack for short-read and long-read genomics projects. Versions are pinned at kickoff and cited in the Methods draft.
| Tool | Version | Role | Primary citation |
|---|---|---|---|
| BWA-MEM2 | 2.2.1 | Short-read alignment to GRCh38 | [6] — https://doi.org/10.1109/IPDPS.2019.00041 |
| GATK | 4.6.0.0 | Duplicate marking, BQSR, variant calling, VQSR | [1] — https://doi.org/10.1002/0471250953.bi1110s43 |
| Picard | 3.2.0 | MarkDuplicates, coverage metrics | [1] — https://doi.org/10.1002/0471250953.bi1110s43 |
| samtools / bcftools | 1.21 | BAM indexing, VCF manipulation | Li et al., 2009 — https://doi.org/10.1093/bioinformatics/btp352 |
| mosdepth | 0.3.3 | Fast coverage depth and breadth | Pedersen & Quinlan, 2018 — https://doi.org/10.1101/517435 |
| Ensembl VEP | 112 | Variant consequence annotation | [7] — https://doi.org/10.1186/s13059-016-0974-4 |
| DeepVariant | 1.8.0 | Neural-network SNV/indel caller (optional) | [8] — https://doi.org/10.1038/nbt.4235 |
| Manta | 1.6.0 | SV discovery from paired reads | Chen et al., 2016 — https://doi.org/10.1093/bioinformatics/btv710 |
| DELLY | 1.2.6 | SV and indel calling | Rausch et al., 2012 — https://doi.org/10.1093/bioinformatics/bts378 |
| minimap2 | 2.28 | Long-read alignment | [3] — https://doi.org/10.1093/bioinformatics/bty191 |
| Clair3 | 1.0.9 | Long-read SNV/indel calling | Zheng et al., 2022 — https://doi.org/10.1038/s41467-022-32121-6 |
| MultiQC | 1.25 | Aggregated QC reporting | [9] — https://doi.org/10.1093/bioinformatics/btw354 |
Teams outsourcing genomics analysis often run into pipeline reproducibility, caller disagreement, CNV/SV detection variability, storage cost, and undocumented filters [5, 13, 14].
Pan et al. [14] tested 56 aligner-caller combinations and found pipelines had a larger impact on inherited-variant reproducibility than platform or library prep. Pepkio pins versions and documents parameters.
Pan et al. [14] found SNV reproducibility varies across pipelines; complementary filters or callers can reduce disagreement. Pepkio applies documented GATK or DeepVariant filters and discusses multi-caller strategies when needed.
Gabrielaite et al. [13] found WGS outperforms WES and suggested combining GATK gCNV, Lumpy, DELLY, and cn.MOPS. Pepkio scopes multi-tool workflows at kickoff.
Regier et al. [3] showed CRAM reduces a 30× WGS BAM from ~54 Gb to ~17 Gb (>3-fold). Pepkio delivers CRAM or compressed VCF where agreed.
Koboldt [5] emphasizes rigorous filtering and benchmarking. Pepkio exports VCF FILTER labels and drafts Methods with exact versions.
Provide paired-end FASTQ or coordinate-sorted BAMs, sample metadata, and a target reference build. Clinical WGS guidelines recommend agreeing on mean coverage and callability metrics at kickoff [4], often around 30x depth with over 95% callability. MD5 checksums are requested at transfer. Non-standard inputs are scoped at kickoff.
Single-sample germline projects typically take 2-4 weeks; multi-sample cohorts with joint genotyping and VQSR typically take 4-8 weeks. CNV/SV or long-read add-ons can extend timelines. Milestones are confirmed at kickoff.
Deliverables include filtered VCFs, annotation tables, coverage QC summaries, PDF/SVG figures, MultiQC HTML, commented scripts with lock files, and a Methods draft. Bespoke formats such as plink exports, IGV sessions, and custom gene lists are agreed at kickoff.
Illumina NovaSeq X, 6000, NextSeq 2000, and HiSeq use BWA-MEM2 + GATK. MGI DNBSEQ-T7, G400, and G99 FASTQs are processed when scoped at kickoff with adapter/QC validation in the report. Element AVITI and Ultima UG100 are processed when scoped at kickoff. PacBio Revio and Oxford Nanopore route to the long-read spoke (minimap2, Clair3).
Sub-threshold libraries are flagged before calling. Low Q30, high adapter content, or depth below agreed thresholds can reduce callable fraction [4]. Pepkio discusses re-sequencing versus stricter filters before proceeding.
Yes. You retain full ownership. Pepkio delivers commented bash, R, and Python scripts with lock files via private Git or agreed transfer, with notebooks available on request.
Yes. Checkpoint reviews occur after alignment QC, after coverage assessment, and before delivery. A PhD-level bioinformatician is your primary contact.
Clarification of methods, QC thresholds, and minor figure or table revisions for analyses we performed are included. Substantial new reviewer-requested analyses are scoped separately.
Pepkio defaults to GRCh38 with GATK bundle 4.6 [2] and alternate loci [3]. GRCh37/hg19 is supported on request for legacy cohorts.
Yes. Client BAMs, custom references, plink exports, somatic extensions, and workflows outside the five spokes are scoped at kickoff with documented deliverables.
Deep-dive pages for specific genomics & variant analysis methods and workflows.
Tell us:
We'll tell you:
Contact us to start with a free consultation. Need everyday bench calculators? Try our free lab tools.
