Jit
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GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3214 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
By Jit 2258 days agoftp.genomics.org.cn - RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2849 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
By Abhimanyu Singh 2764 days agobioinfo-csi.nus.edu.sg - From list of genes... ... to microRNAs Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA...ONT assembly and Illumina polishing pipeline
By Jit 3029 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 3020 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2995 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...ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
By Rahul Nayak 2808 days agofaculty.cse.tamu.edu - With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from...MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2674 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2602 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...
