github.com - DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
Our work is published in Scientific Reports:
Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous...
We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with...
github.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses.
Careful encoding of graph entities allows odgi to efficiently...
There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:
SPAdes: An assembler specifically designed for...
ratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.
It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...
www.ncbi.nlm.nih.gov - Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome...
github.com - SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
More at
https://github.com/jts/sga
SGA...
bioinf.spbau.ru - Ultimate tool for resolving repeats in genome assemblies.
Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module...