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Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3490 days agoStructural variation caller tools using long readsGRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3421 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2886 days agosamstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...FiNGS: Filters for Next Generation Sequencing
By Neel 2045 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...
Libraries or management tools for high throughput sequencing data
Last updated 730 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...1mb long DNA with Nanopore technology
By Jit 3210 days agoLongest read of 1mb achievements with NanoporePacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2883 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2967 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing...
By Jit 3048 days agogithub.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2433 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...
