BOL

github.com - Tools to create plots showing N-statistics for genome assemblies More at https://github.com/dentearl/n50PlottingTools

elp.ucdavis.edu - Generic Genome Browser Version 2: A Tutorial for Administrators This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD,...

catchenlab.life.illinois.edu - Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps...

Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output.

github.com - PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.   More at https://github.com/neufeld/pandaseq

sfu-compbio.github.io - SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any...

www.broadinstitute.org - As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such...

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,...