Rahul Nayak
A Bioinformatician
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FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2756 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...GMASS: a novel measure for genomeassembly structural similarity
By Abhimanyu Singh 2519 days agobioinfo.konkuk.ac.kr - The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 2253 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2136 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...liftover
By Jitendra Narayan 3680 days ago Comments (1)github.com - Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at...RNA-Seq De novo Assembly Using Trinity
By Surabhi Chaudhary 3636 days agogithub.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...DISCOVAR
By Abhimanyu Singh 3610 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...Blobology
By Jit 3554 days agogithub.com - Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh Goal: To create blobplots or...HGA
By Jit 3385 days agogithub.com - HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler...Standardized velvet assembly report
By Poonam Mahapatra 3375 days agogithub.com - Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate...
