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Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 2572 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...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2524 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...MCAT: Motif Combining and Association Tool
By Neel 2143 days agogithub.com - This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional...National Center for Bioinformatics (NCB)
NCB is offering M.Phil and Ph.D programs in the area of Bioinformatics. The major goal of NCB is to promote quality training and research in the area of Bioinformatics. Bioinformatics originated as a cross-disciplinary field as the need for...TRITEX sequence assembly pipeline for Triticeae genomes
By Jit 1924 days agotritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...Senior Research Fellow at NIT, Rourkela
NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA – 769 008(ORISSA) SPONSORED RESEARCH, INDUSTRIAL CONSULTANCY & CONTINUING EDUCATION ADVERTISEMENT NO: NITR/SR/CH-BIF/2014/30 Applications are invited on prescribed format for the following...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 1746 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:MEGADOCK 4.0
By Suleman Khan 3763 days agobioinformatics.oxfordjournals.org - An ultra–high-performance protein–protein docking software for heterogeneous supercomputers Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics...PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
By BioStar 1565 days agogithub.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...
