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My commonly used commands in Bioinformatics
Last updated 2314 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...-
Next generation sequencing in R or bioconductor environment
Last updated 3829 days ago by John Parker Comments (3)There are many R software and bioconductor packages for NGS data analysis, some of them are as follows Biostrings The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It... 
Bioinformatics algorithms tutorials
By John Parker 3807 days agowww.homolog.us - Useful bioinformatics tutorial, such as De Bruijn Graphs for NGS AssemblyAlgorithms for PacBio ReadsSoftware and Hardware Concepts for BioinformaticsFinding us in Homolog.us (Search Algorithms)NGS Genome and RNAseq Assembly - a Hands on...Orione – a web-based framework for NGS analysis in microbiology
By Martin Jones 3778 days agohttp://orione.crs4.it/ - End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that...Shasta long read assembler
By Jit 1777 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...Swabs to Genomes: A Comprehensive Workflow
By Rahul Nayak 3760 days agopeerj.com - The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide...PostDoc Scientist Bioinformatics at CCMB
1. Project Assistant/Junior Research Fellow/ Project Fellow [PA_JRF_PF] a) M.Sc/or equivalent in biological sciences/related areas [Position Code: PA_JRF_PF_a] b) B.E/B.Tech/ M.Sc in biotechnology/bioinformatics/computer...VCF Compare !
By Rahul Nayak 1041 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...ArrayGen Bioinformatics Genomics Group
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PI: ArrayGen Technologies
By ArrayGen Technologies 3711 days agoArrayGen is a global bioinformatics company which is a one stop solution for microarray designing and genomics data analysis. Our novel Array Design Approach Strategy (ADAS) aims to condense the time lag between demands of scientific community and...Postdoc position in protein annotation and machine learning - Paris, France
We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of Paris. Research...
