Rahul Nayak
A Bioinformatician
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Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2839 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. Porechop...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2770 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2727 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...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2696 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...ARCS: scaffolding genome drafts with linked reads
By Jit 2637 days agogithub.com - ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 2268 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2223 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2213 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:KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina...
By Jit 2087 days agogithub.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 1899 days agogithub.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...
