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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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Genomic Open-source Breeding informatics initiative
By BioStar 1886 days agocbsugobii05.biohpc.cornell.edu - To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs. To transform breeding by connecting diverse data with precision...bioinformatics workbook
By biogeek 1886 days agobioinformaticsworkbook.org - This books assumes that the reader has some knowledge of biology and basic understanding of the Unix command line. However, for the beginner, the appendix contains introductory material and tips/tricks for common bioinformatic problems, that is...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1890 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...Galaxy Training Resources !
By Jit 1896 days agotraining.galaxyproject.org - Welcome to Galaxy Training! Collection of tutorials developed and maintained by the worldwide Galaxy community TopicTutorials Introduction to Galaxy Analyses 10 Assembly 6 Climate 3 Computational...Genome assembly training tutorial at Galaxy !
By Jit 1896 days ago Comments (1)training.galaxyproject.org - In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull...EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
By Shruti Paniwala 1897 days agogithub.com - EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1897 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 1899 days agogithub.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...maftools : Summarize, Analyze and Visualize MAF Files
By Neel 1900 days agowww.bioconductor.org - With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of...Applied Computational Genomics Course at UU: Spring 2020
By Shruti Paniwala 1900 days agogithub.com - This course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimental genomics data. It will be structured as a series of lectures covering key concepts and...
