misc genomics tools download

This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586
These include
* identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads
* prokaryotic sequence/genome annotation
* RNAseq analysis - normalisation and collation of multiple samples as a group
* RNAseq visualisation

All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis.
Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually.

Features

Genome sequence error correction
Prokaryotic sequence annotation
RNAseq normalisation of multiple samples as a group
RNAseq sample series/time-course visualisation

Project Samples

RNAseq batch normalisation - graph showing constitutive tile selection

RNAseq visualisation in Artemis - CDS features

RNAseq visualisation in Artemis - sequence tiles

Project Activity

See All Activity >

License

Fair License

Follow misc genomics tools

misc genomics tools Web Site

Other Useful Business Software

Our Free Plans just got better! | Auth0

With up to 25k MAUs and unlimited Okta connections, our Free Plan lets you focus on what you do best—building great apps.

You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.

Try free now

Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

Programming Language

Perl

Related Categories

Perl Bio-Informatics Software

Registered

2021-12-06

Similar Business Software

Genome Analysis Toolkit (GATK)

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. The GATK...

See Software
QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench is a powerful solution that works for everyone, no matter the workflow. Cutting-edge technology and unique features and algorithms widely used by scientific leaders in industry and academia make it easy to overcome challenges associated with data analysis....

See Software
Illumina Connected Analytics

Store, archive, manage, and collaborate on multi-omic datasets. Illumina Connected Analytics is a secure genomic data platform to operationalize informatics and drive scientific insights. Easily import, build, and edit workflows with tools like CWL and Nextflow. Leverage DRAGEN bioinformatics...

See Software
Geneious

Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly. Simple sequence assembly and easy editing of contigs. Automatic annotation for gene prediction, motifs, translation, and variant calling. Genotype...

See Software
Illumina DRAGEN Secondary Analysis

The Illumina DRAGEN Secondary Analysis provides accurate, comprehensive, and efficient analysis of next-generation sequencing data. Graph reference genome and machine learning driving unprecedented accuracy. Provides ultra-efficient workflow; can fully process a 34x whole human genome in ~30...

See Software
Evo Designer

Evo Designer is an advanced tool developed by the Arc Institute, leveraging the capabilities of the Evo 2 genomic foundation model to facilitate DNA sequence generation and analysis. This platform enables users to input nucleotide sequences or specify organisms, prompting the model to generate...

See Software