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The MARVEL assembler
By Jit 2424 days agogithub.com - MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2415 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2387 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1791 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtFigeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 97 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2218 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2404 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2299 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2839 days agoStructural variation caller tools using long readsAndi
By Jit 3146 days agobioinformatics.oxfordjournals.org - This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient...
