Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.

ABSTRACT: Transcriptomes are one of the first sources of high-throughput genomic data that have benefitted from the introduction of Next-Gen Sequencing. As sequencing technology becomes more accessible, transcriptome sequencing is applicable to multiple organisms for which genome sequences are unavailable. Currently all methods for de novo assembly are based on the concept of matching the nucleotide context overlapping between short fragments-reads. However, even short reads may still contain biologically relevant information which can be used as hints in guiding the assembly process. We propose a computational workflow for the reconstruction and functional annotation of expressed gene transcripts that does not require a reference genome sequence and can be tolerant to low coverage, high error rates

SUBMITTER: Ptitsyn A 

PROVIDER: S-EPMC4578894 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature