De-novo assembly of a bacterial genome

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Question: De-novo assembly of a bacterial genome

1

18 months ago by

ppurkayastha2010 • 30

ppurkayastha2010 • 30 wrote:

I am trying to assemble a bacterial genome of length 8Mb in orione.crs4.it . I could successfully load the paired-end illumina dataset into the server, but I am unable to do the de-novo assembly for the paired end data using any of the programs.

Could anyone suggest if the tools are working in the galaxy server? or I am doing something wrong? Please share if there is any protocol for de-novo assembly of a bacterial genome?

assembly denovo bacterial genome orione.crs4.it • 631 views

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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by ppurkayastha2010 • 30

2

18 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The fastq data probably needs to be assigned the correct datatype. Tools will not recognize inputs without this.

Support help:

https://galaxyproject.org/support/
https://galaxyproject.org/support/#getting-inputs-right-
https://galaxyproject.org/support/fastqsanger/ << this is where the "how-to" for setting datatype is explained
https://galaxyproject.org/learn/custom-genomes/ << once you have the assembly completed, and wish to use it with tools as a reference genome, this is how

Tutorials and publications related to assembly in Galaxy can be found here:

https://galaxyproject.org/learn/ << section "Tutorials from around the Web" has several that cover assembly
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1039-4 << a specific assembly use-case tool suite within Galaxy

Thanks! Jen, Galaxy team

ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

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