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ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and...

Harness PacBio reads with assemblers https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads #Reads #Assemblers #PacBio

BBTools can do almost everything now !

Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...

Estimate the genome size https://bioinformatics.uconn.edu/genome-size-estimation-tutorial/ #Genome #Size #Estimate

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...

How to Plot a circular overlapping plots, as shown in pic. ? https://cloud.githubusercontent.com/assets/90373/13977453/0ba63268-f0ef-11e5-9b1b-6b0aa587e3ac.jpg I tried following table to plot on http://mkweb.bcgsc.ca/tableviewer/ data C D A...

Circos is a javascript library to easily build interactive graphs in a circular layout. It's based on d3.js. It aims to be a javascript version of the Circos software. You should consider using Circos to show: relationships...

Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following...

#GFA to #Fasta file conversion. $ grep '^S' example.gfa |awk '{print ">"$2; print $3}' > example.fa

Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results. Online version and downloadable software package for offline use (source code in...

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...

Awk is a programming language which allows easy manipulation of structured data and is mostly used for pattern scanning and processing. It searches one or more files to see if they contain lines that match with the specified patterns and then...