Poonam Mahapatra
Bioinformatics Researcher
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MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1488 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1279 days ago Comments (1)academic.oup.com - LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that...OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 601 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...Five key traits to seek out in potential bioinformatics candidates !!!
By Jit 3423 days agoOnce your research group is ready to make a larger investment and hire a bioinformatician to gain a competitive edge, there are several key traits to seek out in potential candidates. The best bioinformatician are:-Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2251 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...De novo Genome Assembly for Illumina Data
By Rahul Nayak 1799 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...Reference Sequence Resource!
By LEGE 1194 days agowww.encodeproject.org - The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse...HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
By Jit 2511 days agogithub.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1697 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...Is reference genome necessary for gene expression study in transcriptome sequencing or for variant...
Started by Rahul Agarwal 4176 days agoLike in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?
