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...
github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.
Canu is...
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...
www.cs.helsinki.fi - LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.
Publication:
L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de...
www.dkfz.de - TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input...
ml.ssu.ac.kr - gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...
http://efs.heiderlab.de/ - The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in...
wego.genomics.org.cn - WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...
biochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references.
Title: Comparison of Short Read De Novo Alignment Algorithms
Author: Nikhil Gopal