Rahul Nayak
A Bioinformatician
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Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1969 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...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 1750 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 in image classification. Unlike...SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 1561 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1352 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...Steps to find palindrome in genomes !
By BioStar 627 days agoPalindromes are sequences of nucleotides that read the same backward as forward.LoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 2786 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...QuorUM: An Error Corrector for Illumina Reads
By BioStar 1755 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...Ruby and BioRuby Tutorials
By Jitendra Narayan 4109 days ago Comments (4)www.codeschool.com - Collections of Ruby and BioRuby learning materials. BioRuby paper link : http://bioinformatics.oxfordjournals.org/content/26/20/2617.abstractPimp your brain: Bioinformatics
By Neel 3749 days agoJan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp...
