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Bioinformatics workflows
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Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research.
9p
visteverogers
24-06-2023
8
2
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The increasing complexity of data streams and computational processes in modern clinical health information systems makes reproducibility challenging. Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. Workflow management systems (WMS) have been widely used in bioinformatics to handle the reproducibility bottleneck.
12p
vighostrider
25-05-2023
2
2
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The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used.
14p
vihagrid
30-01-2023
8
3
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Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology.
18p
viarchimedes
26-01-2022
11
0
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The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case.
11p
spiritedaway36
25-11-2021
8
1
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Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which can efficiently process the raw nanopore reads, support graphical output and interactive visualizations for interpretations of results.
8p
vitzuyu2711
29-09-2021
12
1
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Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it.
18p
vikentucky2711
26-11-2020
10
0
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Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets.
11p
vikentucky2711
26-11-2020
11
0
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A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, −omics hypothesizing.
12p
vikentucky2711
26-11-2020
7
0
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Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level.
7p
vikentucky2711
26-11-2020
8
0
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Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration.
12p
vikentucky2711
26-11-2020
11
0
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Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics.
11p
vikentucky2711
26-11-2020
10
1
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Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies.
9p
vikentucky2711
26-11-2020
6
0
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Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility.
7p
vikentucky2711
26-11-2020
9
1
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Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python.
12p
vikentucky2711
24-11-2020
26
2
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Peptide-spectrum matching is a common step in most data processing workflows for mass spectrometry-based proteomics. Many algorithms and software packages, both free and commercial, have been developed to address this task.
13p
vikentucky2711
24-11-2020
9
1
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Gene and protein interaction experiments provide unique opportunities to study the molecular wiring of a cell. Integrating high-throughput functional genomics data with this information can help identifying networks associated with complex diseases and phenotypes.
22p
vikentucky2711
24-11-2020
18
3
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Workflows, or computational pipelines, consisting of collections of multiple linked tasks are becoming more and more popular in many scientific fields, including computational biology. For example, simulation studies, which are now a must for statistical validation of new bioinformatics methods and software, are frequently carried out using the available workflow platforms.
19p
vikentucky2711
24-11-2020
14
1
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Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.
7p
vikentucky2711
24-11-2020
11
1
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The rapid pace of bioscience research makes it very challenging to track relevant articles in one’s area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year.
11p
vikentucky2711
24-11-2020
10
1
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