This is the Linux app named misc genomics tools whose latest release can be downloaded as misc_genomics_tools_v0.2.zip. It can be run online in the free hosting provider OnWorks for workstations.
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misc genomics tools
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586
* 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.
- Genome sequence error correction
- Prokaryotic sequence annotation
- RNAseq normalisation of multiple samples as a group
- RNAseq sample series/time-course visualisation
This is an application that can also be fetched from https://sourceforge.net/projects/misc-genomics-tools/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.