Rahul Nayak
A Bioinformatician
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ARCS: scaffolding genome drafts with linked reads
By Jit 2167 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...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 1743 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:mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1555 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...Bioinformatics tools for telomere to telomere assembly !
By BioStar 1193 days agooptimize HiFi readsStacks
By Jitendra Narayan 3194 days agocatchenlab.life.illinois.edu - Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps...cutadapt
By Radha Agarkar 3116 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...WgSim
By Jit 3075 days agogithub.com - Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing...BIMA V3: an aligner customized for mate pair library sequencing
By Abhimanyu Singh 2900 days agobioinformatics.oxfordjournals.org - Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...QuorUM: An Error Corrector for Illumina Reads
By Jit 2571 days agojournals.plos.org - Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...Common steps for reads mapping !
By BioStar 625 days agoMapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.
