Rahul Nayak
A Bioinformatician
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Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 1343 days agohttps://github.com/envgen - Useful Metagenomics resourcesCGView.js is a Circular Genome Viewing tool
By LEGE 861 days agohttps://js.cgview.ca/ - CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView. CGView.js is the genome viewer of Proksee, an expert system for genome...The Role of lncRNA in Bioinformatics: Unlocking the Secrets of the Genome
By LEGE 606 days agolncRNAs are the hidden gems of the genome, and bioinformatics is the key to unearthing their full potential. As research progresses, lncRNAs could pave the way for novel diagnostics, targeted therapies, and personalized medicine, revolutionizing...NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design
By BioStar 530 days agoNVIDIA and the Arc Institute have introduced Evo 2, a groundbreaking AI model designed to understand, predict, and generate DNA sequences. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode...Illuminating next generation sequencing data with Go
By Rahul Agarwal 4730 days agotalks.biogo.googlecode.com - Another good lecture for Illumina sequencing data analysis from Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of AdelaideLoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 3404 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...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 2418 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...Comparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4732 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 GopalALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 3019 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2821 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...
