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BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2908 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2648 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2951 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...Metagenomics role in antibiotic resistance
By Rahul Agarwal 4508 days agowww.landesbioscience.com - Related latest article: http://www.nature.com/nature/journal/v509/n7502/pdf/nature13377.pdfsunbeam: A robust, extensible metagenomics pipeline
By Jit 2300 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...Lorikeet: Strain resolver for metagenomics
By BioStar 821 days agogithub.com - Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially...Shinyheatmap
By Jit 3636 days agohttp://shinyheatmap.com/ - Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in...NCBI PSI-BLAST Tutorial
By Jitendra Narayan 4791 days agohttp:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are...Sequencing By Xpansion
By Jitendra Narayan 4128 days agoXpandomer in a single drop reaction to sequence an entire human genome 1000X over.Blobsplorer
By Jit 3765 days agonematodes.org - Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for...
