Jit
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Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2658 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2499 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 581 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2506 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...LRCstats: Long Read Correction Statistics
By Jit 2650 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...medaka: Sequence correction provided by ONT Research
By BioStar 1786 days agogithub.com - medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods...KisSplice
By Jit 3157 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2499 days agogithub.com - PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 2047 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPcoursera genome assembly tutorial
By Jit 2691 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
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