Jit
Enthusiast computational biologist with business dream !!!
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HALC: High throughput algorithm for long read error correction
By Jit 2829 days ago Comments (1)github.com - HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Neel 2657 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful...Now time is come to revolutionize amino acid sequencing by Nanopore technology
By Rahul Agarwal 4352 days agowww.eurekalert.org - Amino acid sequencing by Nanopore recognition tunneling method1mb long DNA with Nanopore technology
By Jit 3000 days agoLongest read of 1mb achievements with NanoporeNanoPack: visualizing and processing long-read sequencing data
By Jit 2766 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2722 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...Comparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4581 days agobiochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil GopalRGFA: powerful and convenient handling of assembly graphs
By Rahul Nayak 2963 days ago Comments (1)www.ncbi.nlm.nih.gov - RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2757 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2531 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...
