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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (637 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1093 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1254 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 (1306 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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CSAR-web: a web server of contig scaffolding using algebraic rearrangements
By BioStar 2157 days agogenome.cs.nthu.edu.tw - CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. CSAR-web can...Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
By BioStar 2158 days agogithub.com - Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly,...QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
By Neel 2166 days agoquartata.csb.pitt.edu - Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 2170 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...Coronavirus Resources !
By Neel 2172 days ago Comments (15)bigd.big.ac.cn - 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific...tinycov: standalone command line utility written in python to plot coverage from a BAM file
By Jit 2175 days agogithub.com - Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user...chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
By Jit 2175 days agogithub.com - Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. Stable version with pip: pip3 install --user chromosight Stable version with conda: conda install -c bioconda -c conda-forge chromosight or, if you want...Magic-BLAST
By Shruti Paniwala 2178 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
By Jit 2180 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 2181 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...
