After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;... -
Variant Analysis and Genome Assembly: Recommended Tools for Next-Level Sequencing Analysis
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50... -
QC, Alignment, and Mapping: Recommended Tools for Next-Level Sequencing Analysis
With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.
Quality control and preprocessing tools
“Garbage in, garbage out” is a popular... -
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... -
FASTA and FASTQ: A Guide to Key File Formats for Sequencing Data
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... -
Metrics that Matter: Important Metrics for Long-Read Sequencing Experiments—Part 2
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... -
Metrics that Matter: Important Metrics for Long-Read Sequencing Experiments—Part 1
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... -
From Algorithms to Assemblies: An Interview with Sequencing Analysis Experts—Part 6
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... -
From Algorithms to Assemblies: An Interview with Sequencing Analysis Experts—Part 5
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... -
From Algorithms to Assemblies: An Interview with Sequencing Analysis Experts—Part 4
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...
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