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Old 09-30-2013, 12:29 PM   #1
Jayakumar S
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Location: India

Join Date: Sep 2013
Posts: 34
Default Whole genome sequence analysis

Hello,
I am new to this forum and presently involved in some of the whole genome sequencing projects and wish to learn the sequence analysis part from the basics.
Gone through the various articles about it. Now I am somewhat familiar with the theoretical basics.
Now I wish to practice the same.
Can anyone let me know the whole genome sequence available online for my self learning as it will be comfortable for me to try with the small genome with my laptop.
Also, please let me know how to proceed further with the open source tools to be used for the quality check and assembly part.

Thanks & regards,
Jayakumar S
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Old 09-30-2013, 08:07 PM   #2
Mariita
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Location: Auburn, Alabama

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I am kind of new to this also, but i just started learning on how to work on the Miseq platform as i will be using it for my study. Let me know if you want us to learn along together.
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Old 09-30-2013, 08:27 PM   #3
Jayakumar S
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yes, mostly I wish to learn the analysis part.
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Old 10-01-2013, 06:09 AM   #4
krobison
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The Short Read Archive at NCBI and the European Nucleotide Archive are two sources of raw datasets. Each equipment manufacturer tends to have datasets on their technical support websites (or in BaseSpace, in the case of Illumina)
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Old 10-01-2013, 08:01 AM   #5
winsettz
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http://www.illumina.com/systems/mise...ific_data.ilmn

The old illumina page to directly download instead of going through basespace is still up.

The old page was

http://web.archive.org/web/201301152...ific_data.ilmn

ftp://ussd-ftp.illumina.com/Data/SequencingRuns/

Last edited by winsettz; 10-01-2013 at 08:05 AM.
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Old 10-02-2013, 04:26 AM   #6
vishnuamaram
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Location: india

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Hey guys,

Welcome to the NGS analysis world.
Your first step with any FASTQ sequence file should be to check the quality using tools like say

FASTQC from Babraham Institute. http://www.bioinformatics.babraham.a...ojects/fastqc/

Go ahead,
Good luck.
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