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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 (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...
- 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/
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Shasta long read assembler
By Jit 1775 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...heatmaply: popular graphical method for visualizing high-dimensional data
By Neel 1778 days agotalgalili.github.io - This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix), and the ability to zoom from the dendrogram. heatmaply also provides an...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1784 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
By Jit 1785 days agoftp.genomics.org.cn - RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error...DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
By Shruti Paniwala 1785 days agogithub.com - DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered...Machine learning training and courses in bioinformatics !
By Rahul Nayak 1788 days ago Comments (1)homes.sice.indiana.edu - Machine learning techniques have been successful in analyzing biological data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. In this class, we will learn basics about probabilistic models...WOS-C Women Scientist Scheme KIRAN-IPR
By Neel 1792 days ago115.112.95.114 - Women Scientist Scheme WOS-C is one among the most coveted programs that Women Scientists in India apply for. It is an initiative started by the Government of India, Department of Science & Technology (DST) to help women scientists in India to...LibsDyogen: Libibrary for comparative genomics
By Jit 1795 days agogithub.com - Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications. Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in...AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome...
By Jit 1796 days agogithub.com - We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.‘dockr’: the R container
By Jit 1796 days agowww.docker.com - dockr 0.8.6 is now available on CRAN. dockr is a minimal toolkit to build a lightweight Docker container image for your R package, in which the package itself is available. The Docker image seeks to mirror your R session as close as possible with...
