github.com - Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of...
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...
www.bioconductor.org - Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of...
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 - pyScaf orders contigs from genome assemblies utilising several types of information:
paired-end (PE) and/or mate-pair libraries (NGS-based mode)
long reads (NGS-based mode)
synteny to the genome of some related species (reference-based...
Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans).
4dgenome.research.chop.edu - Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted...
www.cbcb.umd.edu - VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the...
www.repeatmasker.org - RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat...
github.com - A probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...