Jit
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DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2385 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 2109 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....
Libraries or management tools for high throughput sequencing data
Last updated 671 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...OPERA : Optimal Paired-End Read Assembler
By Jit 3618 days agosourceforge.net - OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a...dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
By Jit 3150 days agowww.ncbi.nlm.nih.gov - While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the...Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 3191 days agogithub.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...String graph based genome assembly software and tools !
By Rahul Nayak 3151 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.QUAST-LG: Versatile genome assembly evaluation
By Jit 2842 days agocab.spbu.ru - QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we...MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2822 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...CANU genome assembly parameters !
By Rahul Nayak 2768 days agoChoose the appropriate parameters to run Canu and run it.
