Latest comments
Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (623 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (784 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (837 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
Tag cloud
Bioinformatics, Genome, NGS, assembly, Analysis, tool, reads, Sequencing, Data, alignment, Sequence, Visualization, R, Pipeline, Computational Biology, Genomics, genomes, Annotation, Long, Tools, Tutorial, Software, Fast, Gene, DNA, Plot, sequences, Genomic, Assemblies, PacBio, Package, Assembler, de novo, Synteny, Learn, read, Chromosome, accurate, Interactive, Perl, nanopore, genes, Program, Web, Scaffolding, Database, Server, Python, Mapping, Comparative
Our Sponsors
All site bookmarks
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
By Jit 1710 days agogithub.com - ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. ProteoClade helps you analyze two...Phytozome v12.1: plant science community hub for accessing palnts genomic data
By Surabhi Chaudhary 1711 days agophytozome.jgi.doe.gov - Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as...JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 1711 days agogithub.com - 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/wikiApollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 1712 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
By Neel 1714 days agogdblab.com - GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 1718 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...SvABA: Structural variation and indel detection by local assembly
By Jit 1718 days agogithub.com - 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 (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 1721 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...U-Plot: Genome U-Plot sample implementation
By Rahul Nayak 1726 days agogithub.com - The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
By Rahul Nayak 1726 days agosysomics.com - 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 steps of clicks. Ab initio training could be performed according to our published...
