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sourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...

github.com - This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each...

In our lab, we seek to characterize and to compare genomes in order to better understand genetic and evolutionary processes linking genotypes to phenotypes. Sequencing and decoding plant genomes have been integral in our approaches. The...

https://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file. Please Cite the Following Grant JR, Enns E, Marinier E,...

www.ncbi.nlm.nih.gov - we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a...

github.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...

github.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...

github.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...

github.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...

github.com - TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long...