www.e-rna.org - R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and...
1000 Genomes data tutorial at ASHG
Structural variants presentation by
Jan Korbel
European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research...
github.com - Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are...
http://shinyheatmap.com/ - Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in...
github.com - HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order...
cutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...
github.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses.
Careful encoding of graph entities allows odgi to efficiently...
There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:
SPAdes: An assembler specifically designed for...
ratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.
It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...