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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (166 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (623 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (783 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 (836 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
By Neel 1155 days agohuttenhower.sph.harvard.edu - Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community...Getting Started with Nextflow
By LEGE 1161 days agocarpentries-incubator.github.io - Introduction to Bioinformatics workflows with Nextflow and nf-core Getting Started with Nextflow Objectives Understand What a workflow management system is. Understand the benefits of using a workflow management system. Explain the benefits of...LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq...
By LEGE 1162 days agogithub.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...HISAT2 Index Files Download !
By LEGE 1163 days ago Comments (1)daehwankimlab.github.io - Resource for downloading all the HISAT2 related files Please cite: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915...Reference Sequence Resource!
By LEGE 1163 days agowww.encodeproject.org - The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse...A guide to machine learning for biologists
By LEGE 1163 days agowww.nature.com - We aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to...RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
By Jit 1168 days agogithub.com - RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold mergingMachine Learning for Genomics
By Jit 1169 days agogithub.com - Module 1: Statistics for genomics (2-8 August 2021) A simple intro to statistical distributions hypothesis testing linear...JUDI: Just Do It
By Jit 1173 days agogithub.com - judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings. https://github.com/ncbi/JUDIbiostarhandbook
By Neel 1183 days agowww.biostarhandbook.com - Nice book collection for bioinformatician ... highly recommended.
