Neel
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medaka: Sequence correction provided by ONT Research
By BioStar 1651 days agogithub.com - medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods...FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
By Jit 2828 days agokakitone.github.io - FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high...proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
By Jit 2516 days agogithub.com - proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to...HALC: High throughput algorithm for long read error correction
By Jit 2362 days ago Comments (1)github.com - HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig...Phased Human Genome Assembly !
By Rahul Nayak 2240 days agoDiploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference GenomesINC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2555 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...Reference-free prediction of rearrangement breakpoint reads
By Neel 2454 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2386 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2378 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2359 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...
