1590 days ago
shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams
...n, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome....1590 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA&...1580 days ago
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
DeepHiC is a GAN-based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few step...1587 days ago
JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wiki1573 days ago
chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
...conda install -c bioconda -c conda-forge chromosight or, if you want to get the latest development version: pip3 install --user -e git+https://github.com/koszullab/chromosight.git...1567 days ago
tinycov: standalone command line utility written in python to plot coverage from a BAM file
...genome coverage plotter. To install the stable version: pip3 install --user tinycov To install the development version: git clone https://github.com/cmdoret/tinycov.git cd t...1567 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
..., the process of tracing the origins of data and its movement through the workflow), and reproducibility. More at https://dahak-metagenomics.github.io/dahak/1550 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of c...1535 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
...of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.1525 days ago