Radha Agarkar
A Bioinformatician
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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 2384 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2358 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...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...Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2266 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...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 PyYAMLjackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1948 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...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Jit 1766 days agogithub.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1742 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...DISCOVAR
By Abhimanyu Singh 3141 days agowww.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...Resolving the complexity of the human genome using single-molecule sequencing
By Rahul Agarwal 3423 days agowww.nature.com - The human genome is arguably the most complete mammalian reference assembly yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. The results in this paper...
