Rahul Nayak
A Bioinformatician
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GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
By Rahul Nayak 2810 days agogithub.com - GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs....Peregrine & SHIMMER Genome Assembly Toolkit
By Abhi 1755 days agogithub.com - Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...CLAW: Chloroplast Long-read Assembly Workflow
By LEGE 958 days agogithub.com - CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore...HDOCK SERVER
By Neel 2303 days agohdock.phys.hust.edu.cn - HDOCK SERVER Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2902 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 3239 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Rahul Agarwal 4110 days ago Comments (1)github.com - GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data.It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant...Nanopore adaptor !
By Jit 2437 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads....NanoPack: visualizing and processing long-read sequencing data
By Jit 2979 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3235 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...
