Genomics Container

The genomics container is a dedicated compute environment for bioinformatics, pre-loaded with alignment, variant calling, quantification, and pipeline orchestration tools. SSH in and start processing data immediately — no installation required.

What’s included

Alignment & mapping: samtools 1.22.1, bcftools 1.22, htslib 1.22.1, bowtie2 2.5.4, BWA, STAR 2.7.11b

Variant calling & analysis: GATK 4.6.2, PLINK 2.0, beagle 5.4, GLIMPSE2 2.0, Picard 3.4.0

Sentieon Genomics Suite 202503.02: High-performance, GATK-compatible variant calling with deterministic results and significantly faster runtimes. Includes quickstart scripts for whole-genome, exome, and tumor/normal pipelines in ~/sentieon_quickstart. Licensed and ready to use out of the box — no separate Sentieon license required.

Quantification & QC: kallisto 0.51.1, MultiQC, cutadapt

Pipeline orchestration: Nextflow 25.10

Data access: sra-toolkit (fastq-dump, fasterq-dump, prefetch)

Languages: Python 3.12 (numpy, pandas, polars, biopython, pysam, scanpy, anndata, scikit-bio, cyvcf2), R with Bioconductor (DESeq2, edgeR, limma, GenomicRanges, rtracklayer, Biostrings), Java (OpenJDK)

Via the Dashboard

1. Sign in at console.carolinacloud.io
2. In the sidebar, click Create then choose Genomics
3. Select your CPU tier — we recommend high-performance for alignment and variant calling workloads
4. Use the sliders to configure vCPUs, RAM, and disk size (see recommendations below)
5. Optionally paste your SSH public key
6. Click Create
7. Once the status changes to “Running”, use the SSH command on the instance card to connect

Via the API

curl -X POST https://console.carolinacloud.io/api/instance/ \
  -H "Authorization: Bearer YOUR_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "resource_type": "container",
    "flavor": "genomics",
    "n_vcpus": 16,
    "mem_gib": 64,
    "disk_size_gib": 500,
    "cpu_tier": "high-performance"
  }'

Optional fields:

Field	Description
name	Human-friendly name (e.g. wgs-pipeline-01)
cpu_tier	general-purpose (default) or high-performance ($0.01/vCPU/hr, recommended for genomics)
public_key	SSH public key for password-less access

Via the CLI

ccloud new container --cpus 16 --ram 64 --disk 500 \
  --flavor genomics \
  --tier high-performance \
  --name wgs-pipeline

Connecting

ssh -p <wan_ssh_port> ccloud@login.carolinacloud.io

The port and password are shown on your instance card. All tools are on $PATH and ready to use immediately.

Resource recommendations

Workload	vCPUs	RAM	Disk	CPU tier
Small panel sequencing	4-8	16-32 GiB	100-200 GiB	General purpose
Whole-exome	8-16	32-64 GiB	200-500 GiB	High performance
Whole-genome (30x)	16-32	64-128 GiB	500-1000 GiB	High performance
RNA-seq (STAR alignment)	16+	64+ GiB	200-500 GiB	High performance
Population genetics (GWAS)	8-16	32-64 GiB	200-500 GiB	Either

STAR alignment requires significant RAM for genome indexing — budget at least 32 GiB for human genome alignment. Whole-genome variant calling with Sentieon or GATK benefits from high-performance CPUs and 16+ cores.

Using Sentieon

Sentieon tools are on your $PATH and the license is pre-configured. Run Sentieon commands directly:

sentieon driver -r reference.fa -i input.bam \
  --algo Haplotyper output.vcf.gz

Quickstart scripts for common workflows are in ~/sentieon_quickstart. These can be used as templates for:

• Germline whole-genome/exome variant calling
• Somatic tumor/normal analysis
• Joint genotyping

Sentieon provides the same variant calling algorithms as GATK but with deterministic results and substantially faster runtimes, making it well-suited for production pipelines on high-performance instances.

Example: WGS pipeline from SRA to VCF

# Download reads from SRA
fasterq-dump SRR12345678 --threads 8

# Align with BWA
bwa index reference.fa
bwa mem -t 16 reference.fa SRR12345678_1.fastq SRR12345678_2.fastq \
  | samtools sort -@ 4 -o aligned.bam
samtools index aligned.bam

# Mark duplicates
picard MarkDuplicates I=aligned.bam O=dedup.bam M=metrics.txt

# Variant calling with Sentieon (fast, deterministic)
sentieon driver -r reference.fa -i dedup.bam \
  --algo Haplotyper variants.vcf.gz

# Or with GATK
gatk HaplotypeCaller -R reference.fa -I dedup.bam -O variants.vcf.gz

# QC report
multiqc .

Live resizing

Need more cores mid-pipeline? Containers support live resizing without stopping:

curl -X PATCH https://console.carolinacloud.io/api/instance/<uuid>/ \
  -H "Authorization: Bearer YOUR_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{"n_vcpus": 32, "mem_gib": 128}'

Scale up for alignment, scale down for overnight analysis — pay only for what you use.