This is the Linux app named primeScaff to run in Linux online whose latest release can be downloaded as primeScaff-v1.6.1_linux_x86_64.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
Download and run online this app named primeScaff to run in Linux online with OnWorks for free.
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- 1. Downloaded this application in your PC.
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- 6. Download the application, install it and run it.
primeScaff to run in Linux online
DESCRIPTIONprimeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to easily load and visualize the results using tools like UGENE (recommended) or artemis.
- Iterative de novo repeat masking using iteratively RECON
- Automatic design of primers around hundreds of gaps in scaffolds in seconds
- Can be used in any assembly pipeline, just need a standard FASTA file
- Solution for de novo assembly projects with no close reference
This is an application that can also be fetched from https://sourceforge.net/projects/primescaff/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.