Archana Malhotra
Computational Biologist
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Understanding kmer !
By BioStar 1760 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 1569 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 +...Installing Bandage on Ubunty !
By Jit 2958 days agoinstructions successfully build Bandage on a fresh installation of Ubuntu 14.04Ryan E. Mills Lab
Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested...Raphael Lab
Raphael Lab research is focused on Bioinformatics and Computational Biology. Current research interests include next-generation DNA sequencing, structural variation, genome rearrangements in cancer and evolution, and network analysis of somatic...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2899 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...BioRG
This research group works on problems from the fields of Bioinformatics, Biotechnology, Data Mining, and Information Retrieval. The group's research projects includes Comparative Genomics of Bacterial genomes, Metagenomics, Genomic databases,...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2820 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 2268 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...LRCstats: Long Read Correction Statistics
By Jit 3081 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...
