EnglishFrenchSpanish

Ad


OnWorks favicon

BisSNP download for Linux

Free download BisSNP Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named BisSNP whose latest release can be downloaded as BisSNP-1.0.0.jar. It can be run online in the free hosting provider OnWorks for workstations.

Download and run online this app named BisSNP with OnWorks for free.

Follow these instructions in order to run this app:

- 1. Downloaded this application in your PC.

- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 3. Upload this application in such filemanager.

- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.

- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 6. Download the application, install it and run it.

BisSNP


Ad


DESCRIPTION

Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP
BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj



Features

  • SNP caller
  • methylation caller
  • Bisulfite-seq/NOMe-seq/RRBS
  • genotyping


Audience

Science/Research


User interface

Command-line


Programming Language

Perl, Java


Categories

Bio-Informatics

This is an application that can also be fetched from https://sourceforge.net/projects/bissnp/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.


Free Servers & Workstations

Download Windows & Linux apps

Linux commands

Free Servers & Workstations

Download Windows & Linux apps

Ad