Script run_contaminant_filter.pl

21 views
Skip to first unread message

David Bars

unread,
Dec 12, 2022, 11:28:04 AM12/12/22
to Microbiome Helper
Hello,

Thank you for your tool that I am trying to use in my data.

I would like to use your Perl script run_contaminant_filter.pl. I've achieved from https://github.com/LangilleLab/microbiome_helper/wiki/Requirements downloading the Bowtie indices for human and virus Phix.

Nevertheless, I cloned your  Github code to a directory of my Linux and appears others Perl scripts such as: concat_lanes.pl, metaphlan_to_stamp.pl, concat_paired_end.pl and run_pear.pl but I am not able to see the run_contaminant_filter.pl.

Also in the github main page does not appear this Perl script. Is it only available via Virtual Box image?

Thanks on advance for your help

David.

Andre Comeau

unread,
Dec 13, 2022, 12:31:14 PM12/13/22
to Microbiome Helper
David,
That was an older script for use in the original Version1 of the SOP, before the use of Kneaddata was implemented. You should be using the Ver2 or Ver3 (current still being perfected) metaG SOPs here:

ANDRÉ M. COMEAU, PhD
Manager • Integrated Microbiome Resource (IMR)
T: 902.494.2684 | E: andre....@dal.ca 

​Address for deliveries:
Dept. of Pharmacology
Tupper Med. Bldg., room 5D
Dalhousie University
5850 College St.
Halifax NS B3H 4R2 
​

Research Associate (Lab Manager)

Morgan Langille Lab • Dept. of Pharmacology
ResearchGate Profile • GoogleScholar Publications


"Without fantasy, there is no science. Without fact, there is no art." - Nabokov
"The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson 
From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of David Bars <dbarsc...@gmail.com>
Sent: Monday, December 12, 2022 12:28 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] Script run_contaminant_filter.pl
 
CAUTION: The Sender of this email is not from within Dalhousie.
--
You received this message because you are subscribed to the Google Groups "Microbiome Helper" group.
To unsubscribe from this group and stop receiving emails from it, send an email to microbiome-hel...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/microbiome-helper/e8ce91f2-803d-4234-832a-5e62e0120e4cn%40googlegroups.com.

David Bars

unread,
Dec 13, 2022, 3:11:48 PM12/13/22
to Microbiome Helper
Bonjour/Dear Dr. André Comeau,

Ok I understand. However for metagenome benchmarking process I am trying to reproduce the article https://link.springer.com/article/10.1007/s40484-018-0142-9  that offers the raw fastq from simulated datasets and it was used VSEARCH + run_contaminant_filter.pl. Is is not possible to obtain this ancient Perl code in order to reproduce the same methodology of the abovementioned article?

Thanks again,

David Bars
ODAP research group
Barcelona.
El dia dimarts, 13 de desembre de 2022 a les 18:31:14 UTC+1, André Comeau va escriure:

Andre Comeau

unread,
Dec 13, 2022, 4:48:35 PM12/13/22
to Microbiome Helper
OK I understand now the reasoning. Can you email me directly at my email below and I'll get the script to you individually.

ANDRÉ M. COMEAU, PhD
Manager • Integrated Microbiome Resource (IMR)
T: 902.494.2684 | E: andre....@dal.ca 

​Address for deliveries:
Dept. of Pharmacology
Tupper Med. Bldg., room 5D
Dalhousie University
5850 College St.
Halifax NS B3H 4R2 
​

Research Associate (Lab Manager)

Morgan Langille Lab • Dept. of Pharmacology
ResearchGate Profile • GoogleScholar Publications


"Without fantasy, there is no science. Without fact, there is no art." - Nabokov
"The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson 
Sent: Tuesday, December 13, 2022 4:11 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: Re: [microbiome-helper] Script run_contaminant_filter.pl
 
Reply all
Reply to author
Forward
0 new messages