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Biological databases !
By BioStar 2406 days ago Comments (4)ftp.ncbi.nih.gov - Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.htmlUnderstanding PacBio
By Jitendra Narayan 3489 days agogithub.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3045 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2324 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 3045 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3469 days agoStructural variation caller tools using long readsAlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 2010 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3204 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2418 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1739 days agoGenome assembly pipeline !
