Tag Archives: trinity

De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current ...

We are pleased to announce that we are accepting applications for the 8th Annual Workshop on Genomics which is being held once again in beautiful Český Krumlov, Czech Republic from 7-20 January, 2018. More information is below and can be ...

De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it ...

With the decreased cost of RNA-Seq, an increasing number of non-model organisms have been sequenced. Due to the lack of reference genomes, de novo transcriptome assembly is required. However, there is limited systematic research evaluating the quality of de novo ...

A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, ...

The Trinity RNA-Seq de novo assembly software has become a popular application for reconstructing transcriptomes from RNA-Seq in the realms of diverse model and non-model organisms. Trinity involves several software modules (Inchworm, Chrysalis, and Butterfly) that operate in sequence, with ...

Transcriptome assembly using RNA-seq data – particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to ...

Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it ...