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fa_first_qc/fastq_screen.conf

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  1. # This is an example configuration file for FastQ Screen

  2. 

  3. ############################

  4. ## Bowtie, Bowtie 2 or BWA #

  5. ############################

  6. ## If the Bowtie, Bowtie 2 or BWA binary is not in your PATH, you can set 

  7. ## this value to tell the program where to find your chosen aligner.  Uncomment 

  8. ## the relevant line below and set the appropriate location.  Please note, 

  9. ## this path should INCLUDE the executable filename.

  10. 

  11. #BOWTIE	/usr/local/bin/bowtie/bowtie

  12. #BOWTIE2 /usr/local/bowtie2/bowtie2

  13. #BWA /usr/local/bwa/bwa

  14. 

  15. 

  16. 

  17. ############################################

  18. ## Bismark (for bisulfite sequencing only) #

  19. ############################################

  20. ## If the Bismark binary is not in your PATH then you can set this value to 

  21. ## tell the program where to find it.  Uncomment the line below and set the 

  22. ## appropriate location. Please note, this path should INCLUDE the executable 

  23. ## filename.

  24. 

  25. #BISMARK	/usr/local/bin/bismark/bismark

  26. 

  27. 

  28. 

  29. ############

  30. ## Threads #

  31. ############

  32. ## Genome aligners can be made to run across multiple CPU cores to speed up 

  33. ## searches.  Set this value to the number of cores you want for mapping reads.

  34. 

  35. THREADS		32

  36. 

  37. 

  38. 

  39. ##############

  40. ## DATABASES #

  41. ##############

  42. ## This section enables you to configure multiple genomes databases (aligner index 

  43. ## files) to search against in your screen.  For each genome you need to provide a 

  44. ## database name (which can't contain spaces) and the location of the aligner index 

  45. ## files.

  46. ##

  47. ## The path to the index files SHOULD INCLUDE THE BASENAME of the index, e.g:

  48. ## /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37

  49. ## Thus, the index files (Homo_sapiens.GRCh37.1.bt2, Homo_sapiens.GRCh37.2.bt2, etc.) 

  50. ## are found in a folder named 'GRCh37'.

  51. ##

  52. ## If, for example, the Bowtie, Bowtie2 and BWA indices of a given genome reside in 

  53. ## the SAME FOLDER, a SINLGE path may be provided to ALL the of indices.  The index 

  54. ## used will be the one compatible with the chosen aligner (as specified using the 

  55. ## --aligner flag).  

  56. ##

  57. ## The entries shown below are only suggested examples, you can add as many DATABASE 

  58. ## sections as required, and you can comment out or remove as many of the existing 

  59. ## entries as desired.  We suggest including genomes and sequences that may be sources 

  60. ## of contamination either because they where run on your sequencer previously, or may 

  61. ## have contaminated your sample during the library preparation step.

  62. ##

  63. ## Human - sequences available from

  64. ## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/

  65. #DATABASE	Human	/data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37

  66. ##

  67. ## Mouse - sequence available from

  68. ## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/

  69. #DATABASE	Mouse	/data/public/Genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37

  70. ##

  71. ## Ecoli- sequence available from EMBL accession U00096.2

  72. #DATABASE	Ecoli	/data/public/Genomes/Ecoli/Ecoli

  73. ##

  74. ## PhiX - sequence available from Refseq accession NC_001422.1

  75. #DATABASE	PhiX	/data/public/Genomes/PhiX/phi_plus_SNPs

  76. ##

  77. ## Adapters - sequence derived from the FastQC contaminats file found at: www.bioinformatics.babraham.ac.uk/projects/fastqc

  78. #DATABASE	Adapters	/data/public/Genomes/Contaminants/Contaminants

  79. ##

  80. ## Vector - Sequence taken from the UniVec database

  81. ## http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html

  82. #DATABASE	Vectors		/data/public/Genomes/Vectors/Vectors

  83. 

  84. DATABASE	Human	/cromwell_root/tmp/fastq_screen_reference/genome

  85. DATABASE	Mouse	/cromwell_root/tmp/fastq_screen_reference/mouse

  86. DATABASE	ERCC	/cromwell_root/tmp/fastq_screen_reference/ERCC

  87. DATABASE	EColi	/cromwell_root/tmp/fastq_screen_reference/ecoli

  88. DATABASE	Adapter	/cromwell_root/tmp/fastq_screen_reference/adapters

  89. DATABASE	Vector	/cromwell_root/tmp/fastq_screen_reference/vector

  90. DATABASE	rRNA	/cromwell_root/tmp/fastq_screen_reference/rRNARef

  91. DATABASE	Virus	/cromwell_root/tmp/fastq_screen_reference/viral

  92. DATABASE	Yeast	/cromwell_root/tmp/fastq_screen_reference/GCF_000146045.2_R64_genomic_modify

  93. DATABASE	Mitoch	/cromwell_root/tmp/fastq_screen_reference/Human_mitoch

  94. DATABASE	Phix	/cromwell_root/tmp/fastq_screen_reference/phix