Rahul Nayak
A Bioinformatician
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Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 723 days agohttps://github.com/envgen - Useful Metagenomics resourcesCGView.js is a Circular Genome Viewing tool
By LEGE 241 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...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1421 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2375 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2287 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2203 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1753 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
By BioStar 1559 days agogithub.com - SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large...HairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 717 days agohal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no...Trimmomatic: A flexible read trimming tool for Illumina NGS data
By Jit 3144 days agowww.usadellab.org - Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10...
