BOL

www.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...

homer.salk.edu - This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER. Setting up your computing environment Retrieving and storing...

http://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...

satsuma.sourceforge.net - Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes,...

Reformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina...

github.com - In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who...

alignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to sequences within the reference genome. Alignment information is stored in the SAM...

ab.inf.uni-tuebingen.de - Microbiome analysis using a single application MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application. Taxonomic analysis using the NCBI taxonomy or a customized...

www.sbgenomics.com - Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development and precision medicine. We build self-improving systems to analyze millions of genomes, including the Graph...

R Graphical Cookbook by Winston Chang A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown...