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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (202 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (659 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (820 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 (872 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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truvari: Structural variant comparison tool for VCFs
By Jit 1641 days agogithub.com - Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics MotivationThe wavefront alignment (WFA) algorithm
By BioStar 1643 days agogithub.com - The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in...Far Manager Commands and Links !
By Jit 1649 days ago Comments (6)www.farmanager.com - Far Manager is a program for managing files and archives in Windows operating systems. Far Manager works in text mode and provides a simple and intuitive interface for performing most of the necessary actions: viewing files and...KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina...
By Jit 1653 days agogithub.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...sunbeam: A robust, extensible metagenomics pipeline
By Jit 1654 days agogithub.com - Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin...Coronavirus SARS-CoV-2
By Shruti Paniwala 1654 days agonanographics.at - Used Nanographics Vj, our real-time molecular visualization and animation software, to create this video showing the structure of the virus. In the video, you can see the latest theory on how the RNA is organized inside of the virus particle. On...HDOCK SERVER
By Neel 1656 days agohdock.phys.hust.edu.cn - HDOCK SERVER Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support...VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening
By BioStar 1658 days agohttps://virtual-flow.org/ - related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM). Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks: VFLP:...AutoDock Vina: an open-source program for doing molecular docking.
By BioStar 1659 days ago Comments (2)http://vina.scripps.edu/ - AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. It is especially effective for protein-ligand...HS3D: Homo Sapiens Splice Sites Dataset
By Jit 1659 days agowww.sci.unisannio.it - HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of...
