For example, we need fast pipelines to interpret epistatic signals identified from high-throughput analyses, perhaps making use of functional annotation to include biological meaning.
This means that big companies like Amazon, Netflix and Google can't pay to have a faster pipeline to deliver their services.
A schematic of the complete WG-FAST pipeline is shown in Fig. 1.
In the WG-FAST pipeline workflow, reads are initially mapped to a reference genome assembly with BWA-MEM and SNPs are called with the UnifiedGenotyper method in GATK.
The Whole Genome Focused Array SNP Typing (WG-FAST) pipeline can identify unknown strains with much less read data than is needed for genome assembly.
We introduced for the first time an ultra-fast pipeline for large-scale comparison and clustering of RNAs according to sequence and structure, which is key to the functional annotation of ncRNAs.
Our WG-FAST pipeline is able to phylogenetically genotype isolates from single isolate sequencing projects, low coverage sequencing projects, or from complex samples with variable coverage, such as metagenomics projects sequenced from human samples.
To test the robustness of the WG-FAST pipeline using a low number of reads, sequence reads were randomly sampled at varied depths (50 100,000 read pairs), from published E. coli datasets (Additional file 4).
To test the utility of the WG-FAST pipeline, approximately 700 E. coli genome assemblies were downloaded from GenBank [ 28]; E. coli was used as the test case due to the large number of assembled genomes in public databases and due to the non-clonal nature of the species [ 29].
We need faster pipelines, such as the one that the Coalition for Epidemic Preparedness Innovations is trying to create, to preemptively develop vaccines for diseases predicted to cause outbreaks in the near future.
