Jit
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PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2835 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...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 3198 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...
Run miniasm assembler on nanopore reads !
Last updated 3004 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2866 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...Jvarkit : Java utilities for Bioinformatics
By Jit 2832 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsPorechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2842 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...JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
By Jit 2811 days agogithub.com - JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2759 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2741 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 2699 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...
