How To Use Python To Automatically Download Dna Sequencing Files

Adjacent-Generation Sequencing

Dna is a molecule that encodes the blueprint of every living organism. DNA is a chain-like molecule of variable length made of 4 edifice blocks, ordinarily called messages. The four letters of Deoxyribonucleic acid are adenine (A), thymine (T), cytosine (C), and guanine (G). Methods that make up one's mind the alphabetic character sequence of DNA molecules are called sequencing. Next-generation sequencing (NGS) is a high-throughput Deoxyribonucleic acid sequencing technology that enables the reading of billions of Deoxyribonucleic acid molecules in parallel. This generates billions of short sequencing reads (~ 150 letters) that are stored in text files in the FASTQ format.

We launched Nebula Explore to create an affordable entry to personal whole genome sequencing. Nebula Explore is a shallow whole-genome sequencing at an boilerplate coverage of 0.4x per base of operations that results in ~ 1.three billion sequenced bases out of ~ half-dozen.iv billion bases in the human genome. In comparing, nigh other personal genomics companies, including 23andMe and AncestryDNA, apply microarray-based genotyping that reads the human genome at only ~ 500,000 positions.

Sequencing Information Processing

The continuous DNA sequence of a man genome tin be computationally reconstructed past using overlaps betwixt short sequencing reads. The reconstruction of a genome can exist facilitated if a reference genome is available to which the sequencing reads can be aligned. Utilization of reference genomes is possible because representatives of a species are genetically highly similar — for instance, any ii human genome sequences are nearly identical. For example, for Nebula Explore we use the human reference genome GRCh37 (hg19). Hereby a sequence alignment tool is used to map short reads stored in a FASTQ file to the GRCh37 reference genome (Figure ane). This generates a Binary Alignment Map (BAM) file and an associated BAI (Binary Alignment Index) file. FASTQ files are typically discarded after generating BAM files since no data is lost during the alignment process. BAM files tin be easily transformed back into FASTQ files, for case using samtools:

samtools fastq input.bam > output.fastq

DNA Variant Calling — Figure i. Reconstructions of a genome by aligning short reads to a reference genome.

After sequencing reads are aligned to a reference genome, the differences between the sequenced genome and the reference genome tin can exist identified. This procedure is called "variant calling" and produces files in the Variant Call Format (VCF). Hereby we impute the unsequenced portion of the genome using a set of reference genomes that was generated by the 1000 Genomes Project. This yields an boilerplate accuracy of ~ 99% per base beyond the whole genome, which is sufficiently high for predicting beginnings and traits. For users who desire to gain insight into disease risks, carrier status and pharmacogenomics nosotros will presently launch our clinical-class whole genome sequencing that achieves higher accuracy by sequencing each position in the genome on boilerplate 30 times.

Exploring Genomic Data

The showtime iteration of Nebula Explore reporting includes prediction of ancestry and 27 dissimilar traits. However, it is important to understand that personal genome sequencing is the beginning of a journey that volition continuously yield more insight, especially as science advances and new discoveries are fabricated. Thus nosotros will be regularly adding new traits to our reports as well as continuously increasing the granularity of our ancestry predictions.

Nosotros also give our users access to their genomic information (BAM, BAI and VCF files) and invite them to explore their data themselves. Considering uploading personal genomic information to third-political party websites poses privacy risks, we want to introduce a few tools that can be used locally on personal computers.

Viewing BAM files with a genome browser

Genome browsers are used for browsing through reads that are aligned to a reference genome sequence and stored in BAM file. Y'all can try out the Interactive Genome Viewer (IGV).

Download IGV for your operating organization and install information technology.
Download your BAM and BAI files through your Nebula Genomics account.
Open IGV and set the reference genome to hg19 (dropdown in the top left) and download it for better performance (Figure 2). To do this go to the menu bar and select "Genomes" → "Load Genome for Server …" → "Human hg19" and check the box for "Download Sequence".
Drag and drib your BAM file into IGV. Your BAI file must be in the same binder as your BAM file.
View your sequencing reads aligned to the reference genome by selecting chromosomes (one) or search by gene names (two) and and so zooming into the sequence (three).

Determining mtDNA haplogroup

Mitochondria are cell organelles that generate well-nigh of the cell'due south supply of chemical energy. Mitochondria as well have their own genome that is passed on by mothers to their children. Human mitochondrial DNA (mtDNA) haplogroups represent the major branch points in the evolutionary path of the female person lineage. It enables the tracing of modern humans dorsum to their origins in Africa and the subsequent spread around the globe (Figure 3).

Effigy 3. mtDNA haplogroups effectually the globe. Adapted from FamilyTreeDNA.

Y'all tin can determine your haplogroup by analyzing mtDNA reads in your BAM file. For this, you can use the BAM Analysis Kit.

Download and launch the BAM Analysis Kit. This tool is available for Windows PCs simply. (Windows troubleshoot)
Choose "M" for mtDNA (1) as shown in Figure 4. Uncheck all other boxes.
Click "Browse" (2) and select your BAM file.
Click Start Analysis. The processing can take up to an hour.
Open the MtDNA_Haplogroup.txt file to find your mtDNA haplogroup.

Converting VCF Files to 23andMe Files

The 23andMe file format is currently the well-nigh pop format for personal genomic data. Thus nigh consumer-focused tools have files in the 23andMe format as input. To use these tools you can convert your VCF file into a file in the 23andMe format. Notation that Nebula Explore VCF files contain much more information than 23andMe files. By converting into the 23andMe format nosotros are discarding a lot of data for the sake of compatibility with ordinarily used tools.

1. Download VCF-to-23andMe. The two scripts in this directory crave Python 3.

2. First, run the data_to_db.py script using your VCF file as input. This generates the genome.db file:

> python3 data_to_db.py input.vcf.gz vcf genome.db

three. Then run db_to_23.py script using the genome.db file as input. This produces a file in the 23andMe format:

> python3 db_to_23.py genome.db blank_v3.txt 23andMe.txt

Calculating Neanderthal DNA Percentage

Neanderthals are an extinct species of humans, who lived within Eurasia until xl,000 years ago. Because Neanderthals accept interbred with modern humans, most people have some Neanderthal DNA in their genome. You can utilise the Ancient Calculator to find out how much of your genome is shared with Neanderthals and other ancient man relatives.

Download and launch Ancient Calculator (Figure v). This tool is available for Windows PCs only.
Select an aboriginal Dna sample that you want to lucifer your genetic data confronting (i). For instance, select "Altai Neanderthal".
Click "BROWSE" and select your genomic data in the 23andMe format that you have generated from your VCF file. The adding takes simply a few seconds.