BioStar
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GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2375 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from...
By Jit 2356 days agogithub.com - Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2287 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2270 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...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2228 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Neel 2189 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...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1762 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...Filtlong: quality filtering tool for long reads
By Radha Agarkar 1656 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...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1556 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...Steps to find palindrome in genomes !
By BioStar 626 days agoPalindromes are sequences of nucleotides that read the same backward as forward.
