BioStar
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Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2375 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...JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
By Shruti Paniwala 1496 days agogithub.com - This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2751 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...SPAdes
By Abhimanyu Singh 3761 days ago Comments (1)bioinf.spbau.ru - SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 3006 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...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2891 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...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2848 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...Filtlong: quality filtering tool for long reads
By Radha Agarkar 2276 days agogithub.com - Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3431 days agoStructural variation caller tools using long readsINC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3174 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...
