Rahul Nayak
A Bioinformatician
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Run miniasm assembler on nanopore reads !
Last updated 3004 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...Jvarkit : Java utilities for Bioinformatics
By Jit 2832 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsCerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2835 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2804 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2699 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...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Neel 2660 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...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2591 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...Biological databases !
By BioStar 2218 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.htmlmixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2027 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...Steps to find palindrome in genomes !
By BioStar 1097 days agoPalindromes are sequences of nucleotides that read the same backward as forward.
