Neel
Bioinformatics Beginner
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Reference-free prediction of rearrangement breakpoint reads
By Neel 3074 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 3006 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 2998 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 2979 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...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2922 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...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2907 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2849 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...
Evaluation of genome assembly software based on long reads
By BioStar 2744 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...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 2406 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 2370 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike...
