Rahul Nayak
A Bioinformatician
Our Sponsors
Related items
ECTOOLS: Long Read Correction and other Correction tools
By Jit 2514 days agogithub.com - Long Read Correction and other Correction tools This package is a loose collection of scripts. To run the correctionroutine see the section below. Descriptions of the other scriptsare at the bottom of this file. Contact: gurtowsk@cshl.edu In...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...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2391 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2375 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2300 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Neel 2188 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...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...SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 1559 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...Stacks
By Jitendra Narayan 3195 days agocatchenlab.life.illinois.edu - Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps...cutadapt
By Radha Agarkar 3116 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...
