Rahul Nayak
A Bioinformatician
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ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2379 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2333 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....
Evaluation of genome assembly software based on long reads
By BioStar 2168 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 1748 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3180 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...YAHA
By Jit 2911 days agowww.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....Pacbio Long Reads Compatible Software and Tools
By Archana Malhotra 2856 days agogithub.com - The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2422 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...Long read assembly workshop !
By Rahul Nayak 2288 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...QuasR: Quantification and annotation of short reads in R
By Neel 1245 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...
