Jit
Enthusiast computational biologist with business dream !!!
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MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2389 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...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2357 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...
My commonly used commands in Bioinformatics
Last updated 2313 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...Post-doctoral Research Assistant in Genetics
Post-doctoral Research Assistant in Genetics Camden, North London £31.1K per annum inclusive of London Weighting This is a fixed term post for 36 months. We wish to recruit a highly motivated, postdoctoral scientist to carry out a BBSRC...Shasta long read assembler
By Jit 1776 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1759 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...Roth Lab
The Roth Lab seeks insight into biological systems through genome- and proteome-scale experimentation and analysis. Current computational interests: Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to...-
Short-read assembly using Spades !
Last updated 1028 days ago by Abhimanyu Singh Comments (2)If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina... Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 3851 days agowww.ploscompbiol.org - Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 2574 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...
