Question: Spades and Ion Torrent Bam files
gravatar for patterh
2.3 years ago by
patterh20 wrote:

In V3.5.0 of Spades on Galaxy, there is a button "Libraries are IonTorrent reads?". Even if you click "Yes", Galaxy will still not allow one to select a bam format file as input. In the Spades command line, the option --iontorrent will allow bam format input. Am I missing something in Galaxy?


fastq input assembly bam spades • 889 views
ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.3 years ago by patterh20
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The current implemented input type by the tool author is FASTQ. Input reads in BAM format are not supported by the tool wrapper.


  • Use the tool as-is for now. NGS: BamTools > Convert, Merge, Randomize BAM will convert to FASTQ. Double check the resulting reads are actually in fastqsanger format, adjust quality score scaling as needed, and make sure that datatype is assigned to the inputs for the tool to recognize them. How-to for all is in the Galaxy wiki here

  • Contact the tool author through the Tool Shed and request that the BAM input choice be added to the tool wrapper. You must be logged in to see this option. It will be located in the upper right corner pull-down menu on the tool's home page.

  • Perhaps do both, so that you can use the tool now with FASTQ inputs then later with BAM inputs (if the enhancement request is accepted/implemented).

Best, Jen, Galaxy team

ADD COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson25k
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