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Related Experiment Video

Updated: Oct 27, 2025

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

SAUTE: sequence assembly using target enrichment.

Alexandre Souvorov¹, Richa Agarwala²

¹NCBI/NLM/NIH/DHHS, 8600 Rockville Pike, Bethesda, MD, 20894, USA.

BMC Bioinformatics

|July 22, 2021

Summary

This summary is machine-generated.

New assemblers, SAUTE and SAUTE_PROT, improve the assembly of challenging repeat regions from Illumina sequencing data. These tools aid in identifying multiple variants and enhance coding sequence discovery for RNA-seq and genomic data.

Keywords:

Antimicrobial resistance De-novo assembly Illumina reads RNA-seq de Bruijn graphs

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Illumina sequencing technology presents challenges in assembling complex genomic regions due to read length and contamination.
Accurate assembly of repeated regions is crucial for various genomic applications.
Identifying multiple well-supported variants is often required for downstream analysis.

Purpose of the Study:

To develop novel assemblers, SAUTE and SAUTE_PROT, for improved assembly of repeat regions.
To enable the identification of multiple well-supported variants using target sequences.
To enhance the assembly of both RNA-seq and genomic data.

Main Methods:

Utilized de Bruijn graphs for read assembly.
Incorporated target sequences (transcripts, proteins, or genomic regions) to guide the assembly process.
SAUTE uses nucleotide sequences, while SAUTE_PROT uses protein sequences as targets.

Main Results:

SAUTE_PROT demonstrated superior performance in identifying coding sequences that translate to benchmark proteins compared to existing RNA-seq assemblers.
SAUTE exhibited higher sensitivity and precision in assembling target genomic regions compared to several established assemblers.
SAUTE showed improved sensitivity over SKESA for genomic region assembly, though with slightly lower precision.

Conclusions:

SAUTE and SAUTE_PROT offer significant improvements for assembling challenging genomic and transcriptomic regions.
The use of target sequences effectively aids in variant detection and enhances assembly accuracy.
These assemblers provide valuable tools for researchers working with Illumina sequencing data, particularly for repeat-rich regions.