BOL

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

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

http://busco.ezlab.org/ - High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures...

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...

github.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...

github.com - methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent...

github.com - Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes...

journals.plos.org - Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for...

drive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW.  UPARSE >OTU clustering for 16S and other marker genes....