using many ABI files

Commands in mothur
1

Hi everyone,
I am new to mothur, but I have been working with sequencing files for quite some time now.
I have ~450 ABI files (.ab1 format) of 16s gene sequences. I got the files by sending 16s rRNA of single bacterial colonies for sequencing. I wish to analyse them using mothur, so I have two questions regarding that:

  1. Can I import these files and also use the quality data embedded in it so mothur could analyze it ? what I mean is that I want to asses the quality of the files using mothur. I know how to do that with sff and qual files but how do I do it if I only have one file (.ab1) that contains both sequence and quality ?
  2. I have 450 files to process. I know I that for loading and merging I need to write each and every file name to load, and that I can use the “-” sign in between file names, but what if I have so many files ? is there a way to tell mother load “*.abi” or merge it ?

Thank you all so much, this software do look awesome and I hope I can use it to my needs!
Adi

2

There’s nothing in mothur to process ab1 files directly. You would have to hand trim the sequences yourself, export them from that program (e.g. Chromas) and then merge them and run them through mothur. This is what was done with the Esophagus analysis example.

Pat