schatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...
github.com - A de novo genome assembly can be summarised b
y a number of metrics, including:
Overall assembly length
Number of scaffolds/contigs
Length of longest scaffold/contig
Scaffold/contig N50 and N90Assembly base composition, in...
My research group consists primarily of computer science graduate students and postdocs with expertise in algorithms, statistical inferences and machine learning, and sharing a passion for understanding fundamental biological problems.
We work in...
github.com - MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.
The assembly process can be summarized as follows:
overlap
patch reads
overlap...
github.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...
github.com - An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is...
www.zhanyuwang.xin - BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the...