Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling
محفوظ في:
| الحاوية / القاعدة: | BMC Bioinformatics vol. 25 (2024), p. 1 |
|---|---|
| المؤلف الرئيسي: | |
| مؤلفون آخرون: | |
| منشور في: |
Springer Nature B.V.
|
| الموضوعات: | |
| الوصول للمادة أونلاين: | Citation/Abstract Full Text Full Text - PDF |
| الوسوم: |
لا توجد وسوم, كن أول من يضع وسما على هذه التسجيلة!
|
MARC
| LEADER | 00000nab a2200000uu 4500 | ||
|---|---|---|---|
| 001 | 3079146991 | ||
| 003 | UK-CbPIL | ||
| 022 | |a 1471-2105 | ||
| 024 | 7 | |a 10.1186/s12859-024-05846-y |2 doi | |
| 035 | |a 3079146991 | ||
| 045 | 2 | |b d20240101 |b d20241231 | |
| 084 | |a 58459 |2 nlm | ||
| 100 | 1 | |a Phumiphanjarphak, Worakorn | |
| 245 | 1 | |a Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling | |
| 260 | |b Springer Nature B.V. |c 2024 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a BackgroundPan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps.ResultsHere, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage's utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage's capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results.ConclusionsEntourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license. | |
| 653 | |a Reliability analysis | ||
| 653 | |a Assembly | ||
| 653 | |a Software | ||
| 653 | |a Oceans | ||
| 653 | |a Data processing | ||
| 653 | |a Sequence analysis | ||
| 653 | |a Quality control | ||
| 653 | |a Metagenomics | ||
| 653 | |a Cell culture | ||
| 653 | |a Bioinformatics | ||
| 653 | |a Workflow | ||
| 653 | |a Chronic infection | ||
| 653 | |a Viruses | ||
| 653 | |a Severe acute respiratory syndrome coronavirus 2 | ||
| 653 | |a Data analysis | ||
| 653 | |a Genomes | ||
| 653 | |a Viral diseases | ||
| 653 | |a Nucleotide sequence | ||
| 653 | |a Drug resistance | ||
| 653 | |a Genetic diversity | ||
| 653 | |a Proteins | ||
| 653 | |a Datasets | ||
| 653 | |a Microorganisms | ||
| 653 | |a Next-generation sequencing | ||
| 653 | |a Gene sequencing | ||
| 653 | |a Conserved sequence | ||
| 653 | |a Target detection | ||
| 653 | |a Taxonomy | ||
| 653 | |a Genomic analysis | ||
| 653 | |a Viral infections | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Aiewsakun, Pakorn | |
| 773 | 0 | |t BMC Bioinformatics |g vol. 25 (2024), p. 1 | |
| 786 | 0 | |d ProQuest |t Health & Medical Collection | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3079146991/abstract/embedded/H09TXR3UUZB2ISDL?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/3079146991/fulltext/embedded/H09TXR3UUZB2ISDL?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3079146991/fulltextPDF/embedded/H09TXR3UUZB2ISDL?source=fedsrch |