Surabhi Chaudhary
A Bioinformatician
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FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1428 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...Understanding kmer !
By BioStar 1193 days agobioinfologics.github.io - What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 445 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...Understanding PacBio
By Jitendra Narayan 2829 days agogithub.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 2573 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2153 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...BEAR: Better Emulation for Artificial Reads
By BioStar 140 days agogithub.com - Created by Stephen Johnson, Brett Trost, Dr. Jeffrey R. Long, Dr. Anthony Kusalik University of Saskatchewan, Department of Computer Science BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads...Alfred: BAM Statistics and Feature Counting
By Jit 2496 days agogear.embl.de - The easiest way to get Alfred is to download a statically linked binary from the Alfred github release page. Alternatively, you can build Alfred from source. Alfred dependencies are included as submodules so you need to do a recursive...mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 1836 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...Compressive Genomics
Started by Rahul Agarwal 4122 days agoThe key to finding a solution is to notice that most genomicsequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In...
