Author Archives: ark0214

User Guide for CloudBurst on Kbase

Michael Schatz, the author of CloudBurst has made his code available on  Sourceforge site and mentions a brief introduction to CloudBurst which goes as follows: “Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing unprecedented demands … Continue reading

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User Guide for Crossbow on Kbase

This guide gives you directions to using Crossbow, a Hadoop enabled software pipeline for whole genome resequencing analysis on Kbase, our private cloud infrastructure. Crossbow is scalable, portable, and automatic Cloud Computing tool for finding SNPs in genomes from short … Continue reading

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Accessing the Hadoop filesystem (HDFS)

Hadoop has it own distributed file system called HDFS which can be accessed with the hadoop utility. The command to access the HDFS is the file system user client command “fs” Type “hadoop fs” on the command line to get … Continue reading

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Logging into the system

The preferred way to access the Systems Biology Knowledgebase computer (sbkbase.ornl.gov) which is a Linux server, is by using a Secure shell (ssh) utility.  There are various ssh utilities available depending on the machine that you are connecting from: If … Continue reading

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