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Magic-BLAST
By Shruti Paniwala 2268 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...New Release of RefSeq !
By Abhi 690 days agohttps://ncbiinsights.ncbi.nlm.nih.gov/2024/07/15/refseq-release-225/
Run miniasm assembler on nanopore reads !
Last updated 3092 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2936 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2930 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2846 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 2829 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...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2787 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2527 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 2308 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 in image classification. Unlike...
