http://genometools.org/ - The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...
We are using a comparative genomics approach to better understand the structure, function and evolution of the human genome. Our group is one of the pioneers in the field of comparative genomics. We proposed the compact genome of the fugu (Takifugu...
github.com - This pipeline performs the following steps:
Assembly of nanopore reads using Canu.
Polish canu contigs using racon (optional).
Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...
github.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...
hpcugent.github.io - EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.A full list of supported software packages is available here.
github.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).
Ra is in...
github.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
Using AlignGraph
AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...