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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (168 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (624 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (785 days ago): Sequencing coverage is defined as the average number of reads that covers...
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SvABA: Genome-wide detection of structural variants and indels by local assembly
By Abhimanyu Singh 2132 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....HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene...
By Jit 2133 days agogithub.com - A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar...ClipCrop: a tool for detecting structural variations with single-base resolution using...
By BioJoker 2134 days agogithub.com - ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated...SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
By BioJoker 2134 days agobioinf.shenwei.me - FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only...Osprey: Network Visualization System
By BioJoker 2134 days agoosprey.thebiogrid.org - Osprey is a software platform for the visualization of complex biological interaction networks. Osprey builds data-rich graphical representations from Gene Ontology (GO) annotated interaction data maintained by the BioGRID. Osprey is...molinspiration: broad range of cheminformatics software tools supporting molecule manipulation
By BioJoker 2134 days agowww.molinspiration.com - Molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation,...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2134 days ago Comments (1)bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...Quick tour of Genetic Algorithms !
By Jit 2137 days ago Comments (1)cran.r-project.org - The R package GA provides a collection of general purpose functions for optimization using genetic algorithms. The package includes a flexible set of tools for implementing genetic algorithms search in both the continuous and discrete...GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various...
By Rahul Nayak 2139 days agolce.biohpc.swmed.edu - GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information. It efficiently constructs gene...UPhO: Scripts for homology and orthology assessment from genomic sequences.
By BioStar 2140 days agogithub.com - UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO...
