Rahul Nayak
A Bioinformatician
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pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3055 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...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 3043 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 3012 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...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2938 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2883 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...
Evaluation of genome assembly software based on long reads
By BioStar 2802 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...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2424 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 2239 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...Bioinformatics tools for telomere to telomere assembly !
By BioStar 1874 days agooptimize HiFi readsSteps to find palindrome in genomes !
By BioStar 1305 days agoPalindromes are sequences of nucleotides that read the same backward as forward.
