HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which is i...equence manipulation Mapping reads to a reference genome Manipulating SAM/BAM alignment files Visualizing data in a genome brows...2947 days ago
mrFAST: Micro Read Fast Alignment Search Tool
mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short r...2947 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to anal...rganisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). M...2944 days ago
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SATSUMA : Highly sensitive whole-genome synteny alignments.
Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only t...res. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days...Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide...2929 days ago
Hagfish - assess an assembly through creative use of coverage plots
Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experime...sist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-se...2922 days ago
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mappi...technologies, low-coverage and exome) in the 1000 Genomes Proj...2922 days ago
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