Eve free ico
Log in to access
Free

EvE Free

Bioinformatics software

Customizable Bioinformatics Software

Preprocessing | Alignment & Mapping | Variant Calling & Discovery | Annotations | Interpretations | Conversions

Create your own pipeline in seconds. Use defaults or define specific parameters. It's your choice!

Meet EvE, the first universal genetic adaptor that aligns, calls, annotates, converts and interprets almost any genetic data file to EvErything. EvE includes a straightforward user interface and powerful, dynamic processing so that using your custom EvE pipeline is effortless and fast.

With EvE, you can create your own custom pipeline within seconds. For example, you can select Isaac for alignment and SamTools for variant calling. Or you can select CutAdapt for pre-processing, TopHat2 for alignment, Isaac for variant calling and SnpEff for annotation. Once you select your pipeline, you can use defaults or easily modify almost any parameter.

You no longer have to worry about whether your computer hardware and servers are powerful enough to process your data. With EvE, you also don't have to worry about bandwidth charges or obscure cloud computing fees. All you need is an internet connection (such as from a laptop or mobile device) and EvE will process your genetic data.

---

EvE Free converts a genome VCF (gVCF) to a regular VCF.

For full EvE functionality, please use EvE Premium.

Free

There are three editions of EvE:

1. EvE Free (this app)

  • Price: Free
  • Performs limited functionality that includes converting a genome VCF into a regular VCF. For full functionality, please use EvE Premium.
  • With just a few clicks, EvE will process your data.

2. EvE Premium

  • Price: $19.99/use
  • All of the features of EvE and:
    • Incredible speed
      • Premium utilizes dedicated multithreaded cluster cloud computing technology to significantly speed up processing so you receive results in a fraction of the time.
    • Interpretation
      • Premium includes the option for interpretation of human genetic data including identification of pathologic variants.
  • Example: converting a whole genome 100GB FASTQ file to VCF using SamTools or GATK can take several days or more but with EvE Premium the conversion time just several hours.

3. EvE Premium Batch

  • Price: $399/use
  • All the features of EvE Premium and
    • batch processing
      • Premium Batch includes the ability to process multiple files at a single time, all with incredible speed.
      • Simultaneously convert a batch of up to 100 whole genomes from FASTQ to VCF in just hours.

EvE v4 supports the following (please note that most functionality is only available in EvE Premium and EvE Premium Batch):

If a conversion is only possible in EvE Premium then this conversion will still appear in EvE Free but will not be able to be selected (it will appear as an 'inactive' selection).

  • FASTQ to gVCF and regular VCF (Supports both single end reads and paired-end reads)
  • FASTA to to gVCF and regular VCF (Supports both single end reads and paired-end reads)
  • FASTQ to BAM
  • FASTA to BAM
  • FASTQ to SAM
  • FASTA to SAM
  • SAM to FASTQ
  • BAM to FASTQ
  • BAM to gVCF (genome VCF) and regular VCF
  • SAM to gVCF (genome VCF) and regular VCF
  • SAM to BAM
  • BAM to SAM
  • BAM to SVG
  • BAM to CRAM
  • SAM to CRAM
  • CRAM to VCF
  • BED to VCF
  • VCF to WT (Wormtable)
  • GVF to VCF
  • gVCF (genome VCF) to VCF
  • Text region lists to VCF: When a region list is supplied then data for those regions will be extracted.
  • CSV to VCF (specific formatting required)
  • TXT to VCF (specific formatting required)
  • FASTA/ FASTQ/ SAM or BAM to Clinical plus VCF: This is Sequencing VCF format file that included calls and no calls data but excludes reference calls.
  • FASTA/ FASTQ/ SAM or BAM to annotated VCF file
  • FASTA/ FASTQ/ SAM/ BAM and VCF file to GVF: Supports converting  Genome Variation Format file
  • FASTA/ FASTQ/ SAM/ BAM and VCF to Wormtable format
  • Array to VCF: Converts a gene array file including 23andMe, Ancestry.com, Family Tree DNA and The Genographic Project (National Geographic) into a VCF file

INPUTS

EvE accepts almost all file formats including .bz2 and .gz compression.

EvE also accepts inputs generated using any reference genome from hg2 through the latest patch releases of GRCh38.

  • FASTA
  • FASTQ
  • SEQUENCE.TXT
  • QSEQ
  • SAM
  • BAM
  • VCF
  • gVCF (genomic VCF)
  • GVF (Genome variant format)
  • WT (Wormtable)
  • TSV (coming soon)
  • CSV
  • TXT
  • 23andMe data file
  • AncestryDNA data file
  • Family Tree DNA data file
  • Genographic Project (National Geographic) data file

 

OUTPUTS

Outputs can be produced using any reference genome of your choice from hg2 through GRCh38.p3. Please note that some outputs are only available in EvE Premium and EvE Premium Batch.

  • FASTA
  • FASTQ
  • SAM
  • BAM
  • VCF
  • VCF with reference SNP IDs (rs<number>) added
  • Annotated VCF (includes reference SNP IDs rs<number>)
  • gVCF (genomic VCF)
  • GVF (Genome variant format)
  • Clinical+ VCF
  • WT (Wormtable)
  • SVG
  • CRAM
  • AVRO
  • TXT (23andMe format)
  • SQLite
  • CNV (vcf file containing copy number variations) (coming soon)
  • SV (vcf file containing structural variants) (coming soon)
  • ADAM (coming soon)
  • GFF3 (coming soon)
  • MongoDB (coming soon)

Integrated Tools
FASTQC
CutAdapt
BWA
Bowtie 2
TopHat

STAR

HISAT
Stampy
SOAP Aligner
segemehl
Isaac Aligner
Isaac Variant Caller
GATK

SAMtools

 BCFtools

 bgzip

 htsfile

 tabix
Platypus

SnpEff (with ANN field)

SnpSift
GEMINI (SQLite2)
CRAM
GVF Generator

Clinical+ VCF

23andMe to VCF

CSV-TXT-XLS-XLSX to VCF

GFF3

Wormtable

HPG BigData (AVRO)

Ensemble tools

 VEP (Variant Effect Predictor)

ClinVar

CRAM

SVG

gvcftools

CAVA

Picard

When you use EvE, your data files and result file(s) will be stored in your Sequencing.com account, which provides free, unlimited storage of genetic data. 

This simple yet secure approach means you no longer have to use your own storage or computing power to conduct genetic analysis and you also no longer have to use USB drives or FTP sites to move and share genetic data.

 

EvE includes an integration of the following:

Samtools

A suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

  1. Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
  2. BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
  3. HTSlib: A C library for reading/writing high-throughput sequencing data

 

GATK (Genome Analysis Toolkit)

GATK analyzes high-throughput sequencing data. The toolkit, which focuses on providing high quality data, offers a wide variety of tools including variant discovery and genotyping. 

 

Isaac Variant Caller

Isaac Variant Caller (IVC) is an analysis package designed to detect SNVs and small indels from the aligned sequencing reads of a single diploid sample.

 

SnpEFF

SnpEFF predicts the effects of genetic variations and also provides annotations. Annotations can simple such as variant name or more complex such as site of variation such as exon, intron and its effect on gene expression.

 

Sequencing.com Scripts

Since EvE offers conversions between different file formats such which is a multistep process at time, we use our own scripts to pipe data and create some file types.

The following use custom scripts developed by Sequencing.com:

  • Clinical plus VCF file generation
  • gVCF to VCF conversion
  • csv and txt conversion to vcf
    • Includes 23andMe, Ancestry.com, National Geographic, Genes for Good and other companies that provide genetic data as csv and txt files
  • vcf conversion to csv and txt
    • Data is converted into csv files compatible with 23andMe format

 

Wormtable (WT)

Wormtable is a format for storing large scale tabular data and interacting with it. It generates an index file as well that can be used repeatedly. Wormtable files are considered very Python friendly and can be used in downstream Python based analysis.

 

GVF

GVF (Genome Variation Format) is gaining popularity as a standard for sequence ontology based datasets. It is a successor of the GFF3 format and includes pragmas for defining sequence alterations at genomic locations as compared to the reference genome.

 

gVCF

Human clinical applications require sequencing information for both variant and non-variant positions, yet there is currently no common exchange format for such data. Genomic VCF (gVCF) addresses this issue. gVCF is a set of conventions applied to the standard variant call format (VCF) that include genotype, annotation and other information across all sites in the genome in a reasonably compact format.

Samtools

  • The Sequence alignment/map (SAM) format and SAMtools Li H., et al., 2009 Bioinformatics 25: 2078-9. [Pubmed]
  • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Li H. Bioinformatics 2011 Nov 1;27(21): 2987-93. Epub 2011 Sep 8. [Pubmed]
  • Multiallelic calling model in bcftools (-m) Danecek P., et al. [Link]
  • Improving SNP discovery by base alignment quality. Li H. Bioinformatics 2011 Apr 15;27(8):1157-8. doi: 10.1093/bioinformatics/btr076. Epub 2011 Feb 13. [Pubmed]
  • Segregation based metric for variant call QC Durbin R. [Link]
  • Mathematical Notes on SAMtools Algorithms Li H. [Link]

 

GATK

  • The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, McKenna A, et al., Genome Research 2010 20:1297-303 [Article] [Pubmed]
  • A framework for variation discovery and genotyping using next-generation DNA sequencing data, DePristo M, et al., Nature Genetics 2011 43:491-498 [Article] [Pubmed]
  • From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline, Van der Auwera GA, et al., Current Protocols in Bioinformatics 2013 43:11.10.1-11.10.33 [Article] [Pubmed]

 

Isaac Variant Caller

  • Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms Bioinformatics June 4, 2013 29(16): 2041-2043 [Article] [Pubmed]
  • Isaac Genome Alignment and Isaac Variant Caller Illumina Technical Support Note. Pub. No. 770-2013-009 Current as of July 3, 2013 [Link]

 

SnpEff

  • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012 Apr-Jun;6(2):80-92. doi: 10.4161/fly.19695. [PubMed]

 

Sequencing.com Scripts

  • Clinical+ VCF [Link]
  • GVF Convertor

 

Wormtable

  • Processing genome scale tabular data with wormtable [Article]

This app is designed for researchers, bioinformatics experts and genomics professionals. The genetic analysis and statements that appear in this app have not been evaluated by the United States Food and Drug Administration. The Sequencing.com website and all software applications (Apps) that use Sequencing.com's website, as well as Sequencing.com's open Application Programming Interface (API), are not intended to diagnose, treat, cure, or prevent any disease.