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3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2552 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 2171 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...dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
By Jit 1959 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...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 1794 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...sunbeam: A robust, extensible metagenomics pipeline
By Jit 1649 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 1464 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...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1109 days agoGenome assembly pipeline !Bactopia: a flexible pipeline for complete analysis of bacterial genomes
By Abhi 198 days agobactopia.github.io - Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia was inspired by Staphopia, a...Surrogate Variable Analysis (SVA)
By Jit 3707 days agoThe sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment.
