Computational methods for transcriptome annotation and quantification using RNA-seq
High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the
transcriptome, allowing for the complete annotation and quantification of all genes and their …
transcriptome, allowing for the complete annotation and quantification of all genes and their …
[HTML][HTML] Assembly algorithms for next-generation sequencing data
The emergence of next-generation sequencing platforms led to resurgence of research in
whole-genome shotgun assembly algorithms and software. DNA sequencing data from the …
whole-genome shotgun assembly algorithms and software. DNA sequencing data from the …
SKESA: strategic k-mer extension for scrupulous assemblies
A Souvorov, R Agarwala, DJ Lipman - Genome biology, 2018 - Springer
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of
microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit …
microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit …
[HTML][HTML] VSEARCH: a versatile open source tool for metagenomics
Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for
processing and preparing metagenomics, genomics and population genomics nucleotide …
processing and preparing metagenomics, genomics and population genomics nucleotide …
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Abstract Motivation: The Illumina paired-end sequencing technology can generate reads
from both ends of target DNA fragments, which can subsequently be merged to increase the …
from both ends of target DNA fragments, which can subsequently be merged to increase the …
FLASH: fast length adjustment of short reads to improve genome assemblies
T Magoč, SL Salzberg - Bioinformatics, 2011 - academic.oup.com
Motivation: Next-generation sequencing technologies generate very large numbers of short
reads. Even with very deep genome coverage, short read lengths cause problems in de …
reads. Even with very deep genome coverage, short read lengths cause problems in de …
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection
The Brassica genus encompasses three diploid and three allopolyploid genomes, but a
clear understanding of the evolution of agriculturally important traits via polyploidy is lacking …
clear understanding of the evolution of agriculturally important traits via polyploidy is lacking …
Toward almost closed genomes with GapFiller
M Boetzer, W Pirovano - Genome biology, 2012 - Springer
De novo assembly is a commonly used application of next-generation sequencing
experiments. The ultimate goal is to puzzle millions of reads into one complete genome …
experiments. The ultimate goal is to puzzle millions of reads into one complete genome …
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
S Gnerre, I MacCallum, D Przybylski… - Proceedings of the …, 2011 - National Acad Sciences
Massively parallel DNA sequencing technologies are revolutionizing genomics by making it
possible to generate billions of relatively short (~ 100-base) sequence reads at very low …
possible to generate billions of relatively short (~ 100-base) sequence reads at very low …
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
D Aird, MG Ross, WS Chen, M Danielsson, T Fennell… - Genome biology, 2011 - Springer
Despite the ever-increasing output of Illumina sequencing data, loci with extreme base
compositions are often under-represented or absent. To evaluate sources of base …
compositions are often under-represented or absent. To evaluate sources of base …