fastq_screen.conf

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## Threads #
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## Genome aligners can be made to run across multiple CPU cores to speed up 
## searches.  Set this value to the number of cores you want for mapping reads.

THREADS		18


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## DATABASES #
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## This section enables you to configure multiple genomes databases (aligner index 
## files) to search against in your screen.  For each genome you need to provide a 
## database name (which can't contain spaces) and the location of the aligner index 
## files.
##
## The path to the index files SHOULD INCLUDE THE BASENAME of the index, e.g:
## /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
## Thus, the index files (Homo_sapiens.GRCh37.1.bt2, Homo_sapiens.GRCh37.2.bt2, etc.) 
## are found in a folder named 'GRCh37'.
##
## If, for example, the Bowtie, Bowtie2 and BWA indices of a given genome reside in 
## the SAME FOLDER, a SINLGE path may be provided to ALL the of indices.  The index 
## used will be the one compatible with the chosen aligner (as specified using the 
## --aligner flag).  
##
## The entries shown below are only suggested examples, you can add as many DATABASE 
## sections as required, and you can comment out or remove as many of the existing 
## entries as desired.  We suggest including genomes and sequences that may be sources 
## of contamination either because they where run on your sequencer previously, or may 
## have contaminated your sample during the library preparation step.
##
DATABASE	Human	/share/lasallelab/genomes/hg38/
DATABASE	Rhesus	/share/lasallelab/genomes/rheMac10/
DATABASE	Mouse	/share/lasallelab/genomes/mm10/
DATABASE	Rat	/share/lasallelab/genomes/rn6/
DATABASE	PhiX	/share/lasallelab/genomes/PhiX/
DATABASE	Lambda	/share/lasallelab/genomes/Lambda/