Jit
Enthusiast computational biologist with business dream !!!
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TEannot
By Jit 3020 days agourgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 724 days agohttps://github.com/envgen - Useful Metagenomics resourcespipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
By LEGE 277 days agogithub.com - ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across...YASRA: Reference based assembler
By Abhimanyu Singh 2825 days agogithub.com - YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a...Tadpole: an assembler, error-corrector, and read-extender
By BioStar 1754 days agojgi.doe.gov - Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is...GAM-NGS: genomic assemblies merger for next generation sequencing
By Jit 2746 days agogithub.com - GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 2523 days agohttps://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
By Rahul Nayak 2371 days agogithub.com - The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 200 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...New born babies get ready to know their whole genome soon!!!
By Rahul Agarwal 4098 days agoSequencing of hundreds of newborns
