SERF De Novo Genome Analysis

Discover Novel Biomarkers
Predictive Disease Markers
Immunotherapy Response Markers
Trinucleotide Expansion Markers
Fingerprint Markers
Unique Telomere Markers

Classify Specimens
Contain Analysis Scope
Reduce Wet Lab Iterations

Inline Stream Processing
Permutations, Clustering
Overlap Stitching
Nucleotide Richness
Repeats Profiling, Masking

Plant Genomics
Clinical Genomics
Pharmaceutical Genomics
Forensic Genomics

Run Analysis on the Cloud

Enabling Targeted Genomics

[SERF] SRR27438213-Gorilla Marker [SERF] Achyranthes-aspera Marker [SERF] Human Y Chromosome Marker [SERF] Helicobacter pylori Marker [SERF] Neuroendocrine carcinoma Marker [SERF] Infiltrating duct adenocarcinoma Marker [SERF] Lymphoma Tumor Marker [SERF] Pancreatic Tumor Marker [SERF] Immunotherapy Response Prediction [SERF] Disease Markers [SERF] BAT Specimen Markers BioSerf Cloud Enabled Bioinformatics

SERF De Novo Genome Analysis

SERF

De novo analysis of Genomic Data to discover novel Biomarkers

SERF MASK

Identification and Masking of repetitive regions of Genomic Data

SERF CLUSTER

Clustering results from distributed SERF Genome Analysis

SERF CHART

Graphical data visualization of SERF Genome Analysis results

SERF DB

Database of Biomarkers from SERF Genome Analysis

SERF - Discover Novel Biomarkers in a Genomic Haystack

SERF De Novo Analysis

SERF - Allium cepa Telomere Discovery

Conventional Wet Lab Approach

Decades with Wet Lab Iterations

SERF Analysis Approach

Days with Cytological Validation!

SERF - Disease Markers

Helicobacter pylori Marker

SAMN02603995

Neuroendocrine carcinoma Marker

SRR2089355

Infiltrating duct adenocarcinoma Marker

SRR2089357

Lymphoma Marker

SRR2089363

Pancreatic Tumor Marker

SRR2089365

Huntington Disease Marker

SRR1747143 Prefrontal Cortex

Myotonic Dystrophy Marker

Skeletal muscle (Biceps Brachii) Specimen

Monkey Pox Disease Marker

Monkey Pox Disease Specimen

SERF - Bacteria Markers

Bacteria Acharyochloris

Bacteria Abyssicoccus

Bacteria Aceltilactobacillus

Bacteria Nostoc Azollae

Bacteria Echinacea Purpurea

Echinacea Purpurea Bacteria

SERF - SARS Cov2 Markers

SARS-Cov-2 BF.7 Omicron Marker

SARS-Cov-2 B.1.1.529-Omicron Marker

SARS-Cov-2 B.1.617.2 Marker

SARS-Cov-2 B.1.577 Marker

SARS-Cov-2 B.1.575 Marker

SARS-Cov-2 B.1.351 Marker

SARS-Cov-2 B.1.117 Marker

SERF - BAT Specimen Markers

BAT Molossus-HLmolMol2

BAT Myotis-HLmyoMyo6

BAT Phyllostomus-HLphyDis3

BAT Rhinolophus-HLrhiFer5

BAT Rousettus-HLrouAeg4

SERF - Human Chromosome Markers

Human Y Chromosome (Microsatellite)

UC Santa Cruz, NA24385, T2T-CHM13v2.0 dataset

Human Y Chromosome (Minisatellite)

UC Santa Cruz, NA24385, T2T-CHM13v2.0 dataset

Human Y Chromosome (Telomere Lagging)

UC Santa Cruz, NA24385, T2T-CHM13v2.0 dataset

Human Y Chromosome (Telomere Leading)

UC Santa Cruz, NA24385, T2T-CHM13v2.0 dataset

SERF - Medicinal Plant Species Markers

Achyranthes-aspera

SERF - Animal Species Markers

SRR27438213-Gorilla

SERF - Immunotherapy Response Prediction

BioSerf Cloud Enabled Bioinformatics

Point and Click Web Interface
Cloud enabled SaaS Platform
Easy to Use Workflows
Secure Anytime Anywhere Access
Encrypted Data
Use as Needed Cloud Servers
Unlimited Data Storage

No Programming to Learn
No Software to Install
No Systems to Setup
No IT knowhow Needed

Focus on Biology

BioSerf Copy Number Variation GATK Workflow

BioSerf Somatic Mutation GATK Workflow

BioSerf RNA-Seq STAR Workflow

BioSerf RNA-Seq TOPHAT Workflow

BioSerf Sequence Alignment Workflow

BioSerf Variant Call Workflow

Sequence CNV and Mutation Analysis

GATK CNV

Genomic analysis for variant discovery, identifying CNV, SNPs and indels in germline DNA and RNAseq data.

GATK MUTECT

Genomic analysis tool for Calling Somatic Mutations in germline DNA and RNAseq data.

GATK PICARD

Manipulation of High Throughput Sequencing data and formats (SAM/BAM/CRAM/VCF).

GATK ILLUMINA

Process Illumina sequencer data for Base Call Metrics, Lane Metrics, Barcodes, Adapters, Other

Sequence Mapping and Alignment

STAR

Alignment of large high-throughput sequencing reads to a reference genome

BWA

Alignment of Short Reads from Next Generation Sequencers to a Reference Genome.

BOWTIE

Alignment of Short Reads from Next Generation Sequencers to a Reference Genome.

BOWTIE2

Fast Alignment of Short Reads from Next Generation Sequencers to a Reference Genome.

Sequence Variant Analysis

VCFTOOLS

Analytics and utilities for Variant Calling using VCF data.

BCFTOOLS

Analytics and utilities for CNVs, Consensus, Annotations and other Variant Calling using VCF or BCF data.

SAMTOOLS

Manipulation of read alignments including sorting, merging, indexing, retrieval of reads and Mpileups.

DNA and Protein Sequences Alignment

MUMMER

Fast Alignment of pair of genomes or set of sequences or reads against reference genome

NUCMER

Alignment of Mammalian, Bacterial, Eukaryote Genomes

PROMER

Fast protein alignment with six frame amino acid translation of DNA input

Nanopore Sequence Assembly and Consensus Analysis

WTDBG ASSEMBLER

De novo sequence assembler for long reads produced by Oxford Nanopore Technologies (ONT)

WTPOA CONSENSUS

Consensus generator for long reads produced by Oxford Nanopore Technologies (ONT)

CANU ASSEMBLER

Assembler for high-noise single-molecule sequences from Oxford Nanopore Technologies (ONT)

MINIMAP2 ALIGNER

Pairwise alignment (with CIGAR) of long reads produced by Oxford Nanopore Technologies (ONT)

Sequence Quality and Trimming

FASTQC

A high throughput Quality Control analysis of sequenced reads

CUTADAPT

Remove adapter sequences from high-throughput sequencing reads.

CUFFLINKS

Transcript assembly, differential expression, and differential regulation for RNA-Seq.

WGSIM

Generation of sequenced reads from a reference genome with SNPs and INDEL polymorphisms.

Use As Needed Cloud Servers

Cloud Server Control

Cloud Server Use

Countries

Institutions

Analysis

Access

MBases

Deployment Models

BioSerf Analytics with BioSerf Cloud

BioSerf Bioinformatics for De Novo Genome Analysis. Use BioSerf's Amazon AWS cloud compute servers to analyze genome datasets generated by onsite or offsite NGS. Maintain security and privacy of all analytics and results. No hardware or software to install. Access analysis tools and monitor runs using laptops, desktops or mobile devices. Web User Interface without need for Linux System or Command Line Interface knowhow enables focus on biology.

Deploy

BioSerf Analytics with Onsite NGS

BioSerf Bioinformatics for De Novo Genome Analysis. Use your private compute servers and onsite NGS genome datasets. Maintain security and privacy of all analytics and results. No hardware or software to install. Access analysis tools and monitor runs using laptops, desktops or mobile devices. Web User Interface without need for Linux System or Command Line Interface knowhow enables focus on biology.

Deploy

BioSerf Analytics with Offsite NGS

BioSerf Bioinformatics for De Novo Genome Analysis. Use your private compute servers and offsite NGS genome datasets. Maintain security and privacy of all analytics and results. No hardware or software to install. Access analysis tools and monitor runs using laptops, desktops or mobile devices. Web User Interface without need for Linux System or Command Line Interface knowhow enables focus on biology.

Deploy

SERF De Novo Genome Analysis

SERF De Novo Genome Analysis

SERF

SERF MASK

SERF CLUSTER

SERF CHART

SERF DB

SERF - Discover Novel Biomarkers in a Genomic Haystack

SERF De Novo Analysis

SERF - Allium cepa Telomere Discovery

SERF - Disease Markers

SERF - Bacteria Markers

SERF - SARS Cov2 Markers

SERF - BAT Specimen Markers

SERF - Human Chromosome Markers

SERF - Medicinal Plant Species Markers

SERF - Animal Species Markers

SERF - Immunotherapy Response Prediction

Sequence CNV and Mutation Analysis

GATK CNV

GATK MUTECT

GATK PICARD

GATK ILLUMINA

Sequence Mapping and Alignment

STAR

BWA

BOWTIE

BOWTIE2

Sequence Variant Analysis

VCFTOOLS

BCFTOOLS

SAMTOOLS

DNA and Protein Sequences Alignment

MUMMER

NUCMER

PROMER

Nanopore Sequence Assembly and Consensus Analysis

WTDBG ASSEMBLER

WTPOA CONSENSUS

CANU ASSEMBLER

MINIMAP2 ALIGNER

Sequence Quality and Trimming

FASTQC

CUTADAPT

CUFFLINKS

WGSIM

Use As Needed Cloud Servers

Deployment Models

BioSerf Analytics with BioSerf Cloud

BioSerf Analytics with Onsite NGS

BioSerf Analytics with Offsite NGS

ANALYTICS

ANALYTICS

ANALYTICS

ANALYTICS

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