www.bx.psu.edu - We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map...
github.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....
github.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...
The School of Biotechnology offers a curriculum that reflects the multidisciplinary nature of Biotechnology, integrating theoretical and applied science in undergraduate and graduate courses. The school has six departments with about 300 employees,...
The purpose of this cheat sheet is to introduce biologist and bioinformatician to the frequently used tools for NGS analysis as well as giving experience in writing one-liners.
File System ls — list items in current directory ls...
github.com - The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in...
Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Academic
https://academic.oup.com/bioinformatics/article/30/18/2559/2475628 Reference-free SNP detection: dealing with the data...
github.com - MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw...