Rahul Agarwal
I'm a Bioinformatician and Programmer
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Your stress/depression came from ancestor
By Rahul Agarwal 4537 days agoStress drives changes in the sperm microRNA which carry forward to later generationsGeneProf: analysis of high-throughput sequencing experiment
By Jit 3379 days agowww.geneprof.org - GeneProf is a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; "Next-Generation Sequencing" or NGS): Next-gen analysis for next-gen data! Some of...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3234 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 3065 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 3038 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2982 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2959 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate...
By Jit 2937 days agocode.google.com - d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively)...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2883 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLNGS Platforms launched by BGI’s MGI Tech
By Jit 2825 days agoMGI, a subsidiary of global genomics leader BGI Group, announced pricing and its first early access customer for the new ultra high-throughput sequencer, MGISEQ-T7, saying it has driven down sequencing cost to $5 per gigabyte
