Assembly of metatranscriptomic data

Aragion

Junior Member

Join Date: Dec 2016

Posts: 3
- Share
- Tweet
#1

Assembly of metatranscriptomic data

02-03-2017, 04:02 AM

Hello.
I have a set of reads produced by metatranscriptomic cDNA sequensing of the total RNA sample. I need to assemble the RNA-virus genome, which was detected in this sample by the RT-PCR-analysis, using some reference sequence from GenBank and the reads. Can you give me some advise on how to perform this task.
Thanks.
Tags: assembly
maubp

Peter (Biopython etc)

Join Date: Jul 2009

Posts: 1544
- Share
- Tweet
#2

02-10-2017, 09:28 AM

You could try a reference guided assembly, perhaps using MIRA?

You might want to first try mapping all the reads against the reference (with relaxed mapping settings) in order to divide the reads into those which might be part of your virus (mapped to the reference) or not (unmapped).
Comment

Previous template Next

From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data

by SEQadmin2

Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...
- Channel: Articles
Yesterday, 10:05 AM
Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends

by SEQadmin2

With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

Introduction

Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
- Channel: Articles
05-22-2026, 06:42 AM
Environmental Genomics in the Age of NGS: From Microbes to Conservation Strategies

by SEQadmin2

Studying ecosystems means dealing with complex, multi-species communities that are hard to observe at scale. This complexity, however, hides many important questions to be answered, from how biogeochemical cycles work and how climate change can affect species distribution to how conservation strategies can work best.

Genomics, particularly since the expansion of NGS, has transformed ecosystem ecology. By sequencing environmental DNA, we can now assess biodiversity without direct...
- Channel: Articles
05-06-2026, 09:04 AM

Topics	Statistics	Last Post
Long-Read RNA Sequencing Uncovers a Hidden Layer of Immune Cell Regulation by SEQadmin2 Started by SEQadmin2, Yesterday, 12:03 PM	0 responses 19 views 0 reactions	Last Post by SEQadmin2 Yesterday, 12:03 PM
DNA Methylation Study Reveals How Epigenetic Changes Pass Between Generations by SEQadmin2 Started by SEQadmin2, Yesterday, 11:40 AM	0 responses 14 views 0 reactions	Last Post by SEQadmin2 Yesterday, 11:40 AM
MetaBeeAI Helps Scientists Process Research Literature Faster by SEQadmin2 Started by SEQadmin2, 05-28-2026, 11:40 AM	0 responses 29 views 0 reactions	Last Post by SEQadmin2 05-28-2026, 11:40 AM
Scientists Solve a 25-Year Mystery in RNA Interference by SEQadmin2 Started by SEQadmin2, 05-26-2026, 10:12 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 05-26-2026, 10:12 AM

Unconfigured Ad

Assembly of metatranscriptomic data

Comment

Latest Articles

ad_right_rmr

News