Replace bwa indexes by bowtie2 indexes and update fastq-screen config in same way

config/config.yaml

@@ -74,8 +74,8 @@ fastq-screen:
   config: 'config/fastq-screen.conf' # path to the fastq-screen configuration file
   subset: '10000' # Don't use the whole sequence file, but create a temporary dataset of this specified number of read (default: '100000', set '0' for all dataset)
   aligner:
-    - 'bwa'      #
-    #- 'bowtie'  #
-    #- 'bowtie2' #
+    #- 'bwa'     # Burrows-Wheeler Aligner, for mapping low-divergent sequences against a large reference genome
+    #- 'bowtie'  # Bowtie, an ultrafast, memory-efficient short read aligner
+    - 'bowtie2' # Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
 
 ## ---------------------------------------------------------------------------------------------------

config/fastq-screen.conf

@@ -8,8 +8,9 @@
 ## Please note, this path should INCLUDE the executable filename.
 
 BOWTIE	  /usr/local/bowtie
-BOWTIE2	  /usr/local/bowtie2-2.3.4.1/bowtie2
-BWA	  /usr/local/bwa
+#BOWTIE2	  /usr/local/bowtie2-2.3.4.1/bowtie2
+BOWTIE2	  .snakemake/conda/db59fc2b/bin/bowtie2
+#BWA	  /usr/local/bwa
 BWA	  .snakemake/conda/db59fc2b/bin/bwa
 
 ############################################
@@ -55,34 +56,34 @@ THREADS 1
 ##DATABASE	Arabidopsis	 resources/databases/bwa/Arabidopsis/Arabidopsis_thaliana_t10
 ##
 ## Ecoli - sequence available from EMBL accession U00096.2
-DATABASE	Ecoli	 resources/databases/bwa/Ecoli/Echerichia_coli_U00096
+DATABASE	Ecoli	 resources/databases/bowtie2/Ecoli/Echerichia_coli_U00096
 ##
 ##-----
 ## PhiX - sequence available from Refseq accession NC_001422.1
-DATABASE	PhiX	 resources/databases/bwa/Phix/PhiX
+DATABASE	PhiX	 resources/databases/bowtie2/Phix/PhiX
 ##
 ## Adapters - sequence derived from the FastQC contaminats file found at: www.bioinformatics.babraham.ac.uk/projects/fastqc
-DATABASE	Adapters        resources/databases/bwa/Adapters/Adapters
+DATABASE	Adapters        resources/databases/bowtie2/Adapters/Adapters
 ##
 ## Vector - Sequence taken from the UniVec database: http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html, BUT, without phi-X174
-DATABASE	Vectors		 resources/databases/bwa/Vectors/UniVec_wo_phi-X174
+DATABASE	Vectors		 resources/databases/bowtie2/Vectors/UniVec_wo_phi-X174
 ##
 ##-----------
 ## Gorilla g4	
-#DATABASE	Gorilla	 resources/databases/bwa/Gorilla/Gorilla_gorilla_g4
+#DATABASE	Gorilla	 resources/databases/bowtie2/Gorilla/Gorilla_gorilla_g4
 ##
 ## Chimpanzee
-#DATABASE	Chimpanzee	 resources/databases/bwa/Chimpanzee/Pan_troglodytes_t3
+#DATABASE	Chimpanzee	 resources/databases/bowtie2/Chimpanzee/Pan_troglodytes_t3
 ##
 ## Bat 10
-#DATABASE	Bat	 resources/databases/bwa/Bat/Pteropus_vampyrus_v1
+#DATABASE	Bat	 resources/databases/bowtie2/Bat/Pteropus_vampyrus_v1
 ##
 ## HIV - HXB2
-DATABASE	HIV	 resources/databases/bwa/HIV/HXB2
+DATABASE	HIV	 resources/databases/bowtie2/HIV/HXB2
 ##
 ## Ebola - sequence available from NCBI accession NC_002549
-DATABASE	Ebola	 resources/databases/bwa/Ebola/ZEBOV
+DATABASE	Ebola	 resources/databases/bowtie2/Ebola/ZEBOV
 ##
 ## SARS-CoV-2 - sequence from Whuhan available from NCBI accession NC_045512.2
-DATABASE	SARS-CoV-2	 resources/databases/bwa/SARS-CoV-2/Wuhan-Hu-1
+DATABASE	SARS-CoV-2	 resources/databases/bowtie2/SARS-CoV-2/Wuhan-WIV04-2019