VCF: A Guide to Key File Formats for Sequencing Data

Variant Call Format (VCF) is an important file format that is specifically used for storing genetic variation data, such as single nucleotide polymorphisms (SNPs), small insertions or deletions (indels), and structural variations. These tab-delimited files contain useful information about the genomic location, reference allele, and alternate allele(s) for each variant. Due to their flexibility, VCF files are widely used in genomics research and are a key component in many genetic...

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Performing successful sequencing analysis requires an understanding of different file formats and how they are used for various applications. Scientists interested in completing their own sequencing analysis should learn the purpose and contents of each format. In the next two articles, we will explore some of the essential file formats used in sequencing data analysis and their significance in the field.

FASTA

The FASTA file format is one of the most...

As a continuation of our last article, we will be covering important metrics related to long-read sequencing technologies. In this article, we focus on metrics relevant to evaluating the success of a Pacific Biosciences (PacBio) sequencing run.

Pacific Biosciences

PacBio has become synonymous with their High Fidelity (HiFi) sequencing. Supported on their Sequel II and IIe instruments, and now expanded to their latest Revio sequencer, HiFi sequencing is built...

Long-read technologies have repeatedly demonstrated their value in genomics research. They’ve been used for improving genome assemblies¹, haplotype phasing², structural variant detection³, and epigenetic analysis⁴, among many other significant applications. When performing long-read sequencing experiments, it’s important to evaluate the success of the sequencing run using different metrics. Some metrics may be more relevant than others depending on the scope of the...

Welcome to part six of our Q&A article series with leading sequencing analysis providers. We’re interviewing these experts to gain helpful insights into their complex analysis processes.

In this final installment of our series, we ask our participants about one of the most important aspects of data analysis, accuracy and reproducibility.

If you’re just joining us, we recommend reviewing the first installment on quality control, the second installme...

This is part five of our Q&A article series with several leading sequencing analysis providers. We’re asking them important questions to learn how they handle different aspects of the analysis process.

In this latest segment of our series, we ask our participants about keeping up with the latest analysis trends.

Look back at the previous questions to review the first installment on quality control, the second installment on assemblies and alignments, the third...

This is part four of our Q&A article series with several leading sequencing analysis providers. We’re interviewing these experts to learn how they handle different aspects of the analysis process.

During this segment of our series, we ask the experts about the intricacies of data visualization.

In the first installment, we learned about quality control, the second installment covered assemblies and alignments, and the third installment focused on transcript...

This is part three of our Q&A article series with our expert sequencing analysis providers. We’re asking them important questions to learn how they handle different aspects of the analysis process.

In this segment of our series, we ask our participants about the complex processes of transcript quantification and differential expression analysis.

Review the first installment to see how they handle the quality control process, or the second installment to see...

This is part two of our Q&A article series where we ask several leading sequencing analysis providers for their approach to important analysis processes.

In this newest segment of our series, we ask our participants about their assessments of assemblies and alignments.

Take a look back at the first installment to review how each provider handles the quality control process of sequencing data. ...

As sequencing technologies and data analysis tools continue to advance, it is more important than ever to ensure your sequencing data is being handled appropriately. Analyzing sequencing data is a complex process and the current platforms are now capable of performing diverse tasks such as assembling genomes, quantifying transcripts, interpreting detailed experiments, and much more. In this Q&A article series, we’re interviewing top sequencing analysis providers to understand the working...