Tag: GC-content
rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses | BMC Bioinformatics
Case study To illustrate and evaluate the functionality of rprimer, two assays targeted at norovirus GI were designed. Assay A: RT-qPCR for quantitative detection of norovirus GI The first task was to design a broadly reactive RT-qPCR assay for quantitative detection. For this, we decided to use the ‘ambiguous’ primer…
Petabase-scale sequence alignment catalyses viral discovery
Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…
PacBio sequencing output increased through uniform and directional fivefold concatenation
Strategy and design of the method We sought to develop a simple method to increase the sequencing capability of PacBio CCS to sequence several diverse DNA libraries ~ 870 bp in length that encoded protein variants originating from a directed evolution campaign. To achieve an increase in the throughput of a PacBio sequencing…
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ?
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ? 0 A colleague of mine have got the following distribution of GC-content for RNAseq. How to interpret bimodal distribution of GC-content for RNAseq ? Does it mean some contamination ? Is there any method to…
