forked from StevenWingett/FastQ-Screen
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathfastq_screen.conf.example
82 lines (69 loc) · 3.3 KB
/
fastq_screen.conf.example
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
# This is an example configuration file for FastQ Screen
############################
## Bowtie, Bowtie 2 or BWA #
############################
## If the Bowtie, Bowtie 2 or BWA binary is not in your PATH, you can set
## this value to tell the program where to find your chosen aligner. Uncomment
## the relevant line below and set the appropriate location. Please note,
## this path should INCLUDE the executable filename.
#BOWTIE /usr/local/bin/bowtie/bowtie
#BOWTIE2 /usr/local/bowtie2/bowtie2
#BWA /usr/local/bwa/bwa
############################################
## Bismark (for bisulfite sequencing only) #
############################################
## If the Bismark binary is not in your PATH then you can set this value to
## tell the program where to find it. Uncomment the line below and set the
## appropriate location. Please note, this path should INCLUDE the executable
## filename.
#BISMARK /usr/local/bin/bismark/bismark
############
## Threads #
############
## 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 8
##############
## DATABASES #
##############
## 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.
##
## Human - sequences available from
## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
#DATABASE Human /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
##
## Mouse - sequence available from
## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
#DATABASE Mouse /data/public/Genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37
##
## Ecoli- sequence available from EMBL accession U00096.2
#DATABASE Ecoli /data/public/Genomes/Ecoli/Ecoli
##
## PhiX - sequence available from Refseq accession NC_001422.1
#DATABASE PhiX /data/public/Genomes/PhiX/phi_plus_SNPs
##
## Adapters - sequence derived from the FastQC contaminats file found at: www.bioinformatics.babraham.ac.uk/projects/fastqc
#DATABASE Adapters /data/public/Genomes/Contaminants/Contaminants
##
## Vector - Sequence taken from the UniVec database
## http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
#DATABASE Vectors /data/public/Genomes/Vectors/Vectors