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config.yaml
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# List of all DNAseq libraries
libraries:
#- 3556_A
#- 3556_B
#- 3556_C
- 4090_A
- 4090_B
- 4090_C
- 4090_D
- 4090_E
- 4090_F
- 4091_A
- 4091_B
- 4091_C
- 4091_D
- 4091_E
- 4091_F
- 4519_A
- 4519_B
- 4519_C
- 4519_D
- 4519_E
- 4519_F
- 4519_G
- 4519_H
- 4615_A
- 4615_B
- 4615_C
- 4615_D
# List shortnames for all species
species:
- Lstr
- Lmag
- LstrMAC
- LstrMIC
- LmagMAC
- LmagMIC
# Allowed values for 'kingdom' parameter in bbmap
barrnap_kingdoms:
- mito
- euk
- bac
# Names of mtrRNA genes for model
ciliate_mt_rRNA:
- mtSSU
- mtLSU
# Quality trim values for read trimming with bbduk
qtrimvals:
- 2
- 28
# DNAseq libraries organized by species
libraries_by_sp:
Lstr:
illumina-bulk:
- 4090_A
- 4090_B
- 4090_C
illumina-sc:
- 4091_C
- 4091_D
Lmag:
illumina-bulk:
- 4090_D
- 4090_E
illumina-sc:
- 4091_E
- 4091_F
LmagMAC:
illumina-bulk:
- 4519_A
- 4519_C
- 4615_A
- 4615_C
pb-ccs:
- 4777_A
- 4916_A
LmagMIC:
illumina-bulk:
- 4519_B
- 4519_D
- 4615_B
- 4615_D
pb-ccs:
- 4777_B
- 4916_B
LstrMAC:
illumina-bulk:
- 4519_E
- 4519_G
LstrMIC:
illumina-bulk:
- 4519_F
- 4519_H
# List of all Loxodes bulk metagenome DNAseq libraries
libraries_lox:
- 4090_A
- 4090_B
- 4090_C
- 4090_D
- 4090_E
# List of all bulk metagenome DNAseq libraries
libraries_mg:
- 4090_A
- 4090_B
- 4090_C
- 4090_D
- 4090_E
- 4090_F
# List of all single-cell DNAseq libraries
libraries_sc:
- 4091_A
- 4091_B
- 4091_C
- 4091_D
- 4091_E
- 4091_F
# List of all FACS sorted DNAseq libraries
libraries_sort:
- 4519_A
- 4519_B
- 4519_C
- 4519_D
- 4519_E
- 4519_F
- 4519_G
- 4519_H
- 4615_A
- 4615_B
- 4615_C
- 4615_D
# List of all RNAseq libraries
libraries_rnaseq:
- 4305_A
- 4305_B
- 4305_C
- 4305_D
- 4305_E
- 4305_F
# RNAseq libraries and sample files for Trinity organized by experiment
experiments_rnaseq:
exp146:
libraries:
- 4305_A
- 4305_B
- 4305_C
- 4305_D
- 4305_E
- 4305_F
sample_file:
workflow/trinity_samples_rnaseq_exp146.txt
species:
Lmag
strain:
Lm5
# Small-RNAseq libraries and sample files for Trinity, organized by experiment
experiments_srnaseq:
exp146:
libraries:
- 4306_A
- 4306_B
- 4306_C
- 4306_D
- 4306_E
- 4306_F
species:
Lmag
strain:
Lm5
# List of all DNAseq raw reads organized by library
reads_raw:
4090_A:
fwd:
- data/reads/4090_A_run579_AAGAGGCA_S491_L007_R1_001.fastq.gz
- data/reads/gDNA41_1_S1_L002_R1_001.fastq.gz
rev:
- data/reads/4090_A_run579_AAGAGGCA_S491_L007_R2_001.fastq.gz
- data/reads/gDNA41_1_S1_L002_R2_001.fastq.gz
4090_B:
fwd:
- data/reads/4090_B_run579_AAGAGGCA_S492_L007_R1_001.fastq.gz
- data/reads/gDNA41_2_S2_L002_R1_001.fastq.gz
rev:
- data/reads/4090_B_run579_AAGAGGCA_S492_L007_R2_001.fastq.gz
- data/reads/gDNA41_2_S2_L002_R2_001.fastq.gz
4090_C:
fwd:
- data/reads/4090_C_run579_AAGAGGCA_S493_L007_R1_001.fastq.gz
- data/reads/gDNA41_3_S3_L002_R1_001.fastq.gz
rev:
- data/reads/4090_C_run579_AAGAGGCA_S493_L007_R2_001.fastq.gz
- data/reads/gDNA41_3_S3_L002_R2_001.fastq.gz
4090_D:
fwd:
- data/reads/4090_D_run579_AAGAGGCA_S494_L007_R1_001.fastq.gz
- data/reads/gDNA41_4_S4_L002_R1_001.fastq.gz
rev:
- data/reads/4090_D_run579_AAGAGGCA_S494_L007_R2_001.fastq.gz
- data/reads/gDNA41_4_S4_L002_R2_001.fastq.gz
4090_E:
fwd:
- data/reads/4090_E_run579_AAGAGGCA_S495_L007_R1_001.fastq.gz
- data/reads/gDNA41_5_S5_L002_R1_001.fastq.gz
rev:
- data/reads/4090_E_run579_AAGAGGCA_S495_L007_R2_001.fastq.gz
- data/reads/gDNA41_5_S5_L002_R2_001.fastq.gz
4090_F:
fwd:
- data/reads/4090_F_run579_AAGAGGCA_S496_L007_R1_001.fastq.gz
rev:
- data/reads/4090_F_run579_AAGAGGCA_S496_L007_R2_001.fastq.gz
4091_A:
fwd:
- data/reads/4091_A_run579_AAGAGGCA_S427_L005_R1_001.fastq.gz
- data/reads/4091_A_run583_AAGAGGCA_S280_L005_R1_001.fastq.gz
rev:
- data/reads/4091_A_run579_AAGAGGCA_S427_L005_R2_001.fastq.gz
- data/reads/4091_A_run583_AAGAGGCA_S280_L005_R2_001.fastq.gz
4091_B:
fwd:
- data/reads/4091_B_run579_AAGAGGCA_S428_L005_R1_001.fastq.gz
- data/reads/4091_B_run583_AAGAGGCA_S281_L005_R1_001.fastq.gz
rev:
- data/reads/4091_B_run579_AAGAGGCA_S428_L005_R2_001.fastq.gz
- data/reads/4091_B_run583_AAGAGGCA_S281_L005_R2_001.fastq.gz
4091_C:
fwd:
- data/reads/4091_C_run579_GTAGAGGA_S429_L005_R1_001.fastq.gz
- data/reads/4091_C_run583_GTAGAGGA_S282_L005_R1_001.fastq.gz
rev:
- data/reads/4091_C_run579_GTAGAGGA_S429_L005_R2_001.fastq.gz
- data/reads/4091_C_run583_GTAGAGGA_S282_L005_R2_001.fastq.gz
4091_D:
fwd:
- data/reads/4091_D_run579_GTAGAGGA_S430_L005_R1_001.fastq.gz
- data/reads/4091_D_run583_GTAGAGGA_S283_L005_R1_001.fastq.gz
rev:
- data/reads/4091_D_run579_GTAGAGGA_S430_L005_R2_001.fastq.gz
- data/reads/4091_D_run583_GTAGAGGA_S283_L005_R2_001.fastq.gz
4091_E:
fwd:
- data/reads/4091_E_run579_GTAGAGGA_S431_L005_R1_001.fastq.gz
- data/reads/4091_E_run583_GTAGAGGA_S284_L005_R1_001.fastq.gz
rev:
- data/reads/4091_E_run579_GTAGAGGA_S431_L005_R2_001.fastq.gz
- data/reads/4091_E_run583_GTAGAGGA_S284_L005_R2_001.fastq.gz
4091_F:
fwd:
- data/reads/4091_F_run579_GTAGAGGA_S432_L005_R1_001.fastq.gz
- data/reads/4091_F_run583_GTAGAGGA_S285_L005_R1_001.fastq.gz
rev:
- data/reads/4091_F_run579_GTAGAGGA_S432_L005_R2_001.fastq.gz
- data/reads/4091_F_run583_GTAGAGGA_S285_L005_R2_001.fastq.gz
4519_A:
fwd:
- data/reads/4519_A_run645_GTCTTACA_S65_L002_R1_001.fastq.gz
- data/reads/4519_A_run646_GTCTTACA_S110_L003_R1_001.fastq.gz
rev:
- data/reads/4519_A_run645_GTCTTACA_S65_L002_R2_001.fastq.gz
- data/reads/4519_A_run646_GTCTTACA_S110_L003_R2_001.fastq.gz
4519_B:
fwd:
- data/reads/4519_B_run645_GCCGCATG_S66_L002_R1_001.fastq.gz
- data/reads/4519_B_run646_GCCGCATG_S111_L003_R1_001.fastq.gz
rev:
- data/reads/4519_B_run645_GCCGCATG_S66_L002_R2_001.fastq.gz
- data/reads/4519_B_run646_GCCGCATG_S111_L003_R2_001.fastq.gz
4519_C:
fwd:
- data/reads/4519_C_run645_CTGCACAT_S67_L002_R1_001.fastq.gz
rev:
- data/reads/4519_C_run645_CTGCACAT_S67_L002_R2_001.fastq.gz
4519_D:
fwd:
- data/reads/4519_D_run645_CGTGTCTA_S68_L002_R1_001.fastq.gz
- data/reads/4519_D_run646_CGTGTCTA_S112_L003_R1_001.fastq.gz
rev:
- data/reads/4519_D_run645_CGTGTCTA_S68_L002_R2_001.fastq.gz
- data/reads/4519_D_run646_CGTGTCTA_S112_L003_R2_001.fastq.gz
4519_E:
fwd:
- data/reads/4519_E_run645_CCGACGTT_S69_L002_R1_001.fastq.gz
rev:
- data/reads/4519_E_run645_CCGACGTT_S69_L002_R2_001.fastq.gz
4519_F:
fwd:
- data/reads/4519_F_run645_CAATGAGC_S70_L002_R1_001.fastq.gz
rev:
- data/reads/4519_F_run645_CAATGAGC_S70_L002_R2_001.fastq.gz
4519_G:
fwd:
- data/reads/4519_G_run645_ATACGGAG_S71_L002_R1_001.fastq.gz
rev:
- data/reads/4519_G_run645_ATACGGAG_S71_L002_R2_001.fastq.gz
4519_H:
fwd:
- data/reads/4519_H_run645_AGATGCTA_S72_L002_R1_001.fastq.gz
rev:
- data/reads/4519_H_run645_AGATGCTA_S72_L002_R2_001.fastq.gz
4615_A:
fwd:
- data/reads/4615_A_run653_GTCTTACA_S447_L006_R1_001.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L006_R1_001_2.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L007_R1_001.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L007_R1_001_2.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L008_R1_001.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L008_R1_001_2.fastq.gz
rev:
- data/reads/4615_A_run653_GTCTTACA_S447_L006_R2_001.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L006_R2_001_2.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L007_R2_001.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L007_R2_001_2.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L008_R2_001.fastq.gz
- data/reads/4615_A_run653_GTCTTACA_S447_L008_R2_001_2.fastq.gz
4615_B:
fwd:
- data/reads/4615_B_run653_GCCGCATG_S448_L006_R1_001.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L006_R1_001_2.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L007_R1_001.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L007_R1_001_2.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L008_R1_001.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L008_R1_001_2.fastq.gz
rev:
- data/reads/4615_B_run653_GCCGCATG_S448_L006_R2_001.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L006_R2_001_2.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L007_R2_001.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L007_R2_001_2.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L008_R2_001.fastq.gz
- data/reads/4615_B_run653_GCCGCATG_S448_L008_R2_001_2.fastq.gz
4615_C:
fwd:
- data/reads/4615_C_run653_CTGCACAT_S449_L006_R1_001.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L006_R1_001_2.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L007_R1_001.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L007_R1_001_2.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L008_R1_001.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L008_R1_001_2.fastq.gz
rev:
- data/reads/4615_C_run653_CTGCACAT_S449_L006_R2_001.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L006_R2_001_2.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L007_R2_001.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L007_R2_001_2.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L008_R2_001.fastq.gz
- data/reads/4615_C_run653_CTGCACAT_S449_L008_R2_001_2.fastq.gz
4615_D:
fwd:
- data/reads/4615_D_run653_CGTGTCTA_S450_L006_R1_001.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L006_R1_001_2.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L007_R1_001.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L007_R1_001_2.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L008_R1_001.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L008_R1_001_2.fastq.gz
rev:
- data/reads/4615_D_run653_CGTGTCTA_S450_L006_R2_001.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L006_R2_001_2.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L007_R2_001.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L007_R2_001_2.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L008_R2_001.fastq.gz
- data/reads/4615_D_run653_CGTGTCTA_S450_L008_R2_001_2.fastq.gz
# List of all raw RNAseq reads, organized by sequence library
reads_rnaseq_raw:
4305_A:
fwd:
- data/reads-rnaseq/4305_A_run623_TAGCTTGT_S88_L003_R1_001.fastq.gz
- data/reads-rnaseq/4305_A_run625_TAGCTTGT_S15_L003_R1_001.fastq.gz
rev:
- data/reads-rnaseq/4305_A_run623_TAGCTTGT_S88_L003_R2_001.fastq.gz
- data/reads-rnaseq/4305_A_run625_TAGCTTGT_S15_L003_R2_001.fastq.gz
4305_B:
fwd:
- data/reads-rnaseq/4305_B_run623_ACTTGATG_S89_L003_R1_001.fastq.gz
- data/reads-rnaseq/4305_B_run625_ACTTGATG_S16_L003_R1_001.fastq.gz
rev:
- data/reads-rnaseq/4305_B_run623_ACTTGATG_S89_L003_R2_001.fastq.gz
- data/reads-rnaseq/4305_B_run625_ACTTGATG_S16_L003_R2_001.fastq.gz
4305_C:
fwd:
- data/reads-rnaseq/4305_C_run623_TCGAGCGT_S90_L003_R1_001.fastq.gz
- data/reads-rnaseq/4305_C_run625_TCGAGCGT_S17_L003_R1_001.fastq.gz
rev:
- data/reads-rnaseq/4305_C_run623_TCGAGCGT_S90_L003_R2_001.fastq.gz
- data/reads-rnaseq/4305_C_run625_TCGAGCGT_S17_L003_R2_001.fastq.gz
4305_D:
fwd:
- data/reads-rnaseq/4305_D_run623_TAGTCTTG_S91_L003_R1_001.fastq.gz
- data/reads-rnaseq/4305_D_run625_TAGTCTTG_S18_L003_R1_001.fastq.gz
rev:
- data/reads-rnaseq/4305_D_run623_TAGTCTTG_S91_L003_R2_001.fastq.gz
- data/reads-rnaseq/4305_D_run625_TAGTCTTG_S18_L003_R2_001.fastq.gz
4305_E:
fwd:
- data/reads-rnaseq/4305_E_run623_TCCAGTCG_S92_L003_R1_001.fastq.gz
- data/reads-rnaseq/4305_E_run625_TCCAGTCG_S19_L003_R1_001.fastq.gz
rev:
- data/reads-rnaseq/4305_E_run623_TCCAGTCG_S92_L003_R2_001.fastq.gz
- data/reads-rnaseq/4305_E_run625_TCCAGTCG_S19_L003_R2_001.fastq.gz
4305_F:
fwd:
- data/reads-rnaseq/4305_F_run623_TTACTCGC_S93_L003_R1_001.fastq.gz
rev:
- data/reads-rnaseq/4305_F_run623_TTACTCGC_S93_L003_R2_001.fastq.gz
# List of all PacBio sequences, organized by sequence library
pb_raw:
4777_A:
# subreads:
ccs:
- data/pb/4777_A_HIFI.fastq.gz
4777_B:
# subreads:
ccs:
- data/pb/4777_B_HIFI.fastq.gz
4916_A:
ccs:
- data/pb/4916_A_HIFI.fastq.gz
- data/pb/4916_A_4777_A3_run538_CCS.fastq.gz
4916_B:
ccs:
- data/pb/4916_B_HIFI.fastq.gz
- data/pb/4916_B_4777_B3_run540_CCS.fastq.gz