2944 days ago
HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which is im...sequence manipulation Mapping reads to a reference genome Manipulating SAM/BAM alignment files Visualizing data in a geno...2944 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 sho...2944 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) prov...e methods enable the analysis of data sets of any size on multi-core desktop computers...lants, animals and even complex samples (e.g. metagenomes). More at https://gatb.in...2942 days ago
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2927 days ago
SATSUMA : Highly sensitive whole-genome synteny alignments.
Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps o...res. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days...lma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly...2927 days ago
Hagfish - assess an assembly through creative use of coverage plots
...amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment. Ha...data set. Hagfish has more power the larger the insert size of the paired end library is....2920 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...g technologies, low-coverage and exome) in the 1000 Geno...2920 days ago