Rahul Agarwal
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SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2285 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate...
By Jit 2256 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 2202 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLNGS Platforms launched by BGI’s MGI Tech
By Jit 2144 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 gigabytejackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1947 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1761 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1488 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....
Libraries or management tools for high throughput sequencing data
Last updated 50 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...How Genes are Regulated: Transcription Factors
By Jitendra Narayan 4097 days agoEach cell in our body inherits the same master copy of DNA, but different cell types use it differently. Transcription Factors help influence which genes are used in which cell. Understanding how these dynamic proteins physically interact with DNA...An entire genome written in lab
By Rahul Nayak 4047 days agoResearchers rewrite an entire genome — and add a healthy twist
