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sunbeam: A robust, extensible metagenomics pipeline
By Jit 1620 days agogithub.com - Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin...Liftoff: An accurate GFF3/GTF lift over pipeline
By Neel 1435 days agogithub.com - Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...JUDI: Just Do It
By Jit 1175 days agogithub.com - judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings. https://github.com/ncbi/JUDISqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 141 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...HiCdat
By Jit 3208 days agogithub.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...KisSplice
By Jit 3022 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...Machine Learning !!!
By Gudiya Pal 3068 days agowww.r2d3.us - In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions. Keep scrolling. Using a data set about homes, we will...WiseScaffolder
By Poonam Mahapatra 3056 days agoabims.sb-roscoff.fr - Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common...CrossMap
By Abhimanyu Singh 3002 days agocrossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10...LUMPY
By Shruti Paniwala 3013 days agogithub.com - A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...
