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Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1570 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.NCBI Datasets pages
By BioStar 664 days agoAssembly and Genome record pages now redirect to new NCBI Datasets pages.Reference Sequence Resource!
By LEGE 1328 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...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2552 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
By Rahul Nayak 1818 days agogithub.com - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2298 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...splitbam: splits a BAM by chromosomes
By Jit 2989 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...Salzberg lab
We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2974 days agoStructural variation caller tools using long readsHISAT2 Index Files Download !
By LEGE 1328 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...
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