japsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...
Scientific Interests:
Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.
Statistical methods for the...
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
Sandelin group have a deep interest in most biology, but focus on gene regulation and the many areas that are connected with this, including transcriptomics, epigenetics and technological and informatics aspects.
The group is both computational...
sourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads.
Cerulean v0.1 has been implemented with bacterial genomes in mind.
The method is fully described in...
Agricultural research in modern scientific arena is being represented by proper integration among various research fields of biological, chemical and physical sciences, because this field encompasses many more complexities of biology in nature. In...
github.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...
A post-doctoral fellowship is available in the research groups of Nick Goldman (EBI) and John Welch (Genetics Department, Cambridge University) under the EMBL-EBI / Cambridge Computational Biomedical Postdoctoral Fellowship scheme.
The project is...
github.com - Call sviper
~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants
This will output a polished_variants.vcf file, that contains all the refined variants.
Sometimes it is helpful to look at the...