Archana Malhotra
Computational Biologist
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Understanding kmer !
By BioStar 1877 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...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1686 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 3257 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...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 3069 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 3037 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Referee: Genome assembly quality scores
By Jit 2895 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...Genome sequence-based (sub-)species delineation.
By Abhimanyu Singh 2857 days agohttp://ggdc.dsmz.de/ - The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C...Nicolas Corradi Lab
The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance. To achieve this goal, our team combines the power of next generation DNA sequencing and...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 3410 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2992 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...
