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runFQSCRN_6_nofish.conf
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# This is a configuration file for FastQ Screen that runs contaminant databases
## Human - sequences available from
DATABASE Human /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
##
## Mouse - sequence available from
## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
##
## Ecoli- sequence available from EMBL accession U00096.2
DATABASE Ecoli /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/Ecoli_GCF_000005845.2_ASM584v2_genomic.fna
##
## PhiX - sequence available from Refseq accession NC_001422.1
#DATABASE PhiX /data/public/Genomes/PhiX/phi_plus_SNPs
DATABASE PhiX /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/phix_nc_001422.1.fasta
##
## Adapters - sequence derived from the FastQC contaminats file found at: www.bioinformatics.babraham.ac.uk/projects/fastqc
#DATABASE Adapters /data/public/Genomes/Contaminants/Contaminants
DATABASE Contamnts_Adaptrs /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/fastqc_contaminant_list.fasta
##
## Vector - Sequence taken from the UniVec database
## http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
DATABASE Vectors /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/UniVec
##
## Microbes
DATABASE Bacteria_24k /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/bacterial_genomes2.fasta
#DATABASE Bacteria_0-5K /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/bacteria_5k.fasta
#DATABASE Bacteria_5-6K /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/bacteria_5-6k.fasta
#DATABASE Bacteria_6-12K /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/bacteria_6-12k.fasta
#DATABASE Bacteria_12-18K /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/bacteria_12-18k.fasta
#DATABASE Bacteria_18-24K /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/bacteria_18-24k.fasta
DATABASE Protists_1k /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/protist_genomes.fasta
DATABASE Viruses /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/viral_genomes.fasta
#DATABASE Fungi /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/fungi_genomes.fasta
#DATABASE Fungi_genRefSeq /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/fungi_genref.fasta
DATABASE Fungi_RefSeq_release /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/fungi_refseq.fasta
##
## Coral, Bird, Plant
DATABASE Coral /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/coral.fasta
DATABASE Bird /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/Columba_livia_GCF_000337935.1_Cliv_1.0_genomic.fna
DATABASE Plant /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/Vanilla_trignocarpa_GCA_016413895.1_Elo_Vpla-A_principal_1.0_genomic.fna
##
## FISH GENOMES
## All fish concatenated
#DATABASE All_Fish /home/e1garcia/shotgun_PIRE/fastq_screen/indexed_databases/allFish.fasta
## Lle, Genomes for Leiognathus - 4 spp - Sciaenids
#DATABASE Leignathidae_genomes /home/e1garcia/PIRE_data/Ssp/noDup_10bp_fq/genomes/Fish/fishgenomescombined/fishgenomescombined.fna
##
## Aur, Genomes for Ambassis - 5 spp - pomacentrids, Mugil
#DATABASE Ambassidae_genomes /home/e1garcia/shotgun_PIRE/fastq_screen/genomes/genomes_ambassis/ambassidae_genomes.fasta
#DATABASE Ambassidae_genomes /home/e1garcia/shotgun_PIRE/fastq_screen/genomes/genomes_ambassis/newA/ambassidae_genomes.fasta
##
## Sob, Genomes for Sphyraena - 5 spp - carangidis, Toxotidae, Xiphiidae
#DATABASE Sphyraenidae_genomes /home/e1garcia/shotgun_PIRE/fastq_screen/genomes/genomes_sphyraena/sphyraenidae_genomes.fasta
##
## Adu, Hte, Genomes for Atherinomorus and Hypoatherina - 5 spp - Poeciliidae, Atherinopsidae, Pachypanchax
#DATABASE Atherinidae_genomes /home/e1garcia/shotgun_PIRE/fastq_screen/genomes/genomes_atherinomorus_hypoatherina/atherinidae_Genm.fasta
##
## Ssp, Genomes for Siganus -
#DATABASE Siganidae_genomes /home/e1garcia/shotgun_PIRE/fastq_screen/genomes/genomes_siganidae/siganidae_genomes.fasta
##
##