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Setting python version as default on Linux
By Rahul Nayak 2319 days agoIf you have a later version than 2.6 you'll need to set 2.6 as the default Python.Nucleus: Python and C++ code for reading and writing genomics data.
By Jit 1803 days agogithub.com - Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework,...Luigi: a Python package that helps you build complex pipelines of batch jobs.
By Neel 1295 days agogithub.com - Luigi is a Python (3.6, 3.7, 3.8, 3.9 tested) package that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization, handling failures, command line integration, and much more. Run pip...scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms,...
By Jit 2505 days agohttp://scikit-bio.org/ - scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear...tinycov: standalone command line utility written in python to plot coverage from a BAM file
By Jit 1753 days agogithub.com - Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user...LUMPY
By Shruti Paniwala 3059 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):...JPred4: A Protein Secondary Structure Prediction Server
By Poonam Mahapatra 2568 days agowww.compbio.dundee.ac.uk - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2413 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1049 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 2617 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...
