Pipelines

ELSA

ELSA

50x coverage WGS (150GB): 4 hours
200x coverage WES (10G): 15 mins

About ELSA

ELSA is an economic, fast and accurate solution for the secondary analysis of next generation sequencing data.

From raw reads to variants, including single nucleotide polymorphism (SNP) and insertion and deletion (INDEL), ELSA takes about 4 hours to process a 50-fold whole genome sequence (WGS) sample, or 10 minutes for a 200-fold whole exome sequence (WES) sample. 

ELSA’s speed is rooted at its parallel algorithms to effectively exploit a CPU SIMD, or a GPU to speed up processes like alignment, score recalibration, INDEL realignment, de-duplication and variant calling. 

ELSA incorporates a 16-genotype model to support the calling of SNPs and INDELs. Validation of the final results with the NIST Genome In A Bottle standard demonstrates that ELSA analysis pipeline has the highest combined sensitivity and precision.

Whole Exome Analysis - BWA + GATK 2.3.9-Lite (with Metrics)

Adapted from sbgenomics.

Whole Exome Analysis - BWA + GATK 2.3.9-Lite

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
Whole Genome Analysis - BWA + GATK 2.3.9-Lite (with Metrics)

Adapted from sbgenomics.

Whole Genome Analysis - BWA + GATK 2.3.9-Lite (with Metrics)

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
RNA-Seq Differential Expression - Cuffdiff (with Visualization)

Adapted from sbgenomics.

RNA-Seq Differential Expression - Cuffdiff (with Visualization)

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
RNA-Seq Alignment - TopHat

Adapted from sbgenomics.

RNA-Seq Alignment
- TopHat

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
RNA-Seq Alignment - STAR

Adapted from sbgenomics.

RNA-Seq Alignment
- STAR

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
WES:Human Whole Exome Sequencing Analysis Pipeline

Developed by BGI

WES:Human Whole Exome Sequencing Analysis Pipeline

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
WGS: Human Whole Genome Sequencing Analysis Pipeline

Developed by BGI

WGS: Human Whole Genome Sequencing Analysis Pipeline

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
RNA-seq : RNA-seq Analysis Pipeline

Developed by BGI

RNA-seq : RNA-seq Analysis Pipeline

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*
Whole Genome Analysis 30x - BWA + GATK

Developed by L3 Bioinformatics

Whole Genome Analysis 30x - BWA + GATK

30x coverage (12GB) ≈ $X*
50x coverage (26GB) ≈ $X*