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Understanding Greedy Algorithms
By Jit 2904 days agowww.topcoder.com - Learning greedy algo for biologist. https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/ This webpage is also useful for the...GAM-NGS: genomic assemblies merger for next generation sequencing
By Jit 2897 days agogithub.com - GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two...
Genome Assembly Tools and Software - PART1 !!
Last updated 2888 days ago by JitThe genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for...PANDASEQ
By Shruti Paniwala 2862 days agoneufeldserver.uwaterloo.ca - PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable...BRIG
By Jit 2838 days agobrig.sourceforge.net - BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available...Prokka: tool for the rapid annotation of prokaryotic genomes
By Jit 2820 days agowww.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and...
By Jit 2819 days agogithub.com - COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore,...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2552 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...MeDuSa: a multi-draft based scaffolder
By Abhimanyu Singh 2475 days agogithub.com - MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...Installing Bandage on Ubunty !
By Jit 2392 days agoinstructions successfully build Bandage on a fresh installation of Ubuntu 14.04
