Rahul Nayak
A Bioinformatician
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RACA: Reference-Assisted Chromosome Assembly
By Priya Singh 3152 days ago Comments (1)bioen-compbio.bioen.illinois.edu - Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end...splitbam: splits a BAM by chromosomes
By Jit 2824 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2384 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Phased Human Genome Assembly !
By Rahul Nayak 2237 days agoDiploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference GenomesrHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2252 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)...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2356 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...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 1747 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2373 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2226 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2387 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...
