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GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 3054 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...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 3012 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2965 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2907 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina...
By Jit 2298 days agogithub.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 2030 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...HairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 1397 days agohal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2833 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...Simulating the Unseen: New Tools Reshaping Metagenomic Research
By LEGE 11 days agoBenchmarking a new metagenomic pipeline often begins with a fundamental challenge. Imagine a bioinformatician preparing to benchmark a new metagenomic pipeline. There is no shortage of real sequencing data, but one problem quickly appears: the exact...Sequencing Solutions to World Health
By Rahul Agarwal 4784 days agowww.lifetechnologies.com - "New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine." Source: Life technologies
