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Old 12-10-2016, 09:59 PM   #3
bloosnail
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Location: Pittsburgh

Join Date: Jul 2015
Posts: 17
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Thank you for the quick response. The idea of assembling the reads into contigs before alignment makes sense, I will let me supervisor know. Do you know of good software to do this? I have tried Velvet in the past but did not use it extensively.

I forgot to mention that we have removed human sequences, although the revised reference genome that you created seems like it would be especially useful for us.

Could you give more information on how to estimate the depth of the bacteria? There is generally less than 100,000 bacterial reads per sample out of 20-30 million initial reads (before any trimming/contaminant removal).
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