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config.yaml
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config.yaml
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rnaseq:
N72:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN72_RunId008_LaneId1/N72_S13_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN72_RunId008_LaneId1/N72_S13_R2_001.fastq.gz
N70:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN70_RunId008_LaneId1/N70_S12_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN70_RunId008_LaneId1/N70_S12_R2_001.fastq.gz
N44:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN44_RunId008_LaneId1/N44_S11_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN44_RunId008_LaneId1/N44_S11_R2_001.fastq.gz
N39:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN39_RunId008_LaneId1/N39_S10_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN39_RunId008_LaneId1/N39_S10_R2_001.fastq.gz
N38:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN38_RunId008_LaneId1/N38_S9_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN38_RunId008_LaneId1/N38_S9_R2_001.fastq.gz
N34:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN34_RunId008_LaneId1/N34_S8_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN34_RunId008_LaneId1/N34_S8_R2_001.fastq.gz
N27:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN27_RunId008_LaneId1/N27_S7_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN27_RunId008_LaneId1/N27_S7_R2_001.fastq.gz
N26:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN26_RunId008_LaneId1/N26_S6_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN26_RunId008_LaneId1/N26_S6_R2_001.fastq.gz
N10:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN10_RunId008_LaneId1/N10_S5_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN10_RunId008_LaneId1/N10_S5_R2_001.fastq.gz
N6:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN6_RunId008_LaneId1/N6_S4_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN6_RunId008_LaneId1/N6_S4_R2_001.fastq.gz
N5:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN5_RunId008_LaneId1/N5_S3_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN5_RunId008_LaneId1/N5_S3_R2_001.fastq.gz
N4:
fwd: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN4_RunId008_LaneId1/N4_S2_R1_001.fastq.gz
rev: /ebio/abt6_sra/years/2021/12_14/karyocode_rnaseq/illumina_VH00745_flowcellAAAJJJCHV_SampleIdN4_RunId008_LaneId1/N4_S2_R2_001.fastq.gz
lstr_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512997_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512997_2.fastq.gz
rema_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512996_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512996_2.fastq.gz
bame_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512973_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512973_2.fastq.gz
anig_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512978_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512978_2.fastq.gz
trac_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512994_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512994_2.fastq.gz
gsin_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513005_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513005_2.fastq.gz
sroe_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513009_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513009_2.fastq.gz
gacu_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513007_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513007_2.fastq.gz
lx13_yy:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512999_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512999_2.fastq.gz
bame2_yy: # Blepharisma americanum
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512974_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512974_2.fastq.gz
tc01_yy: # Trachelocerca sp. Sr_ci_Tc01
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512995_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512995_2.fastq.gz
lstr2_yy: # Loxodes striatus
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512998_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512998_2.fastq.gz
lx11_yy: # Loxodes sp. Sr_ci_Lx11
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513001_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513001_2.fastq.gz
# lx05_yy: # Loxodes sp. Sr_ci_Lx05
# fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513002_1.fastq.gz
# rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513002_2.fastq.gz
kn01_yy: # Kentrophoros sp. Sr_ci_Kn01
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513003_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513003_2.fastq.gz
gl04_yy: # Geleia sp. Sr_ci_Gl04
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513004_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513004_2.fastq.gz
gsin2_yy: # Geleia sinica
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513006_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513006_2.fastq.gz
cx01_yy: # Cryptopharynx sp. Sr_ci_Cx01
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513008_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513008_2.fastq.gz
smin_yy: # Spirostomum minus
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513010_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10513010_2.fastq.gz
cvir_yy: # Climacostomum virens
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512971_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512971_2.fastq.gz
cl01_yy: # Climacostomum sp. Sr_ci_Cl01
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512972_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR10512972_2.fastq.gz
# MMETSP
cmag_mm: # Condylostoma magnum
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1296902_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1296902_2.fastq.gz
pard_mm: # Parduczia sp.
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1300374_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1300374_2.fastq.gz
bjap_mm: # Blepharisma japonicum
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1294460_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1294460_2.fastq.gz
fsal_mm: # Fabrea salina
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1300445_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1300445_2.fastq.gz
cvir_mm: # Climacostomum virens
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1300461_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1300461_2.fastq.gz
# Kentrophoros metatranscriptomes
sa331_kh:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentH_sa331_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentH_sa331_2.fastq.gz
sa332_kh:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentH_sa332_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentH_sa332_2.fastq.gz
s4110_ksd:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentSD_s4110_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentSD_s4110_2.fastq.gz
s4111_ksd:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentSD_s4111_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentSD_s4111_2.fastq.gz
s4112_ksd:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentSD_s4112_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/kentSD_s4112_2.fastq.gz
# Stentor polymorphus
spol_upp:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR6714474_1.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR6714474_2.fastq.gz
rnaseq_bam: # mapped RNAseq reads for genome-guided assembly, already sorted & indexed
bsto: /ebio/abt2_projects/ag-swart-blepharisma-raw/production/B_stoltei_ATCC/MAC/rna-seq/Bsto_ATCC_MAC_cleaned_plus_cruft.merged.bam
rnaseq_se: # single-ended RNAseq sequencing
# scoe: /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR5043309.fastq.gz
bsp_mk : /ebio/abt2_projects/ag-swart-karyocode/data/sra/SRR1614987.fastq.gz
mda:
A19:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/mda/A19_S88_R1_001.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/mda/A19_S88_R2_001.fastq.gz
A25:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/mda/A25_S89_R1_001.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/mda/A25_S89_R2_001.fastq.gz
A31:
fwd: /ebio/abt2_projects/ag-swart-karyocode/data/mda/A31_S90_R1_001.fastq.gz
rev: /ebio/abt2_projects/ag-swart-karyocode/data/mda/A31_S90_R2_001.fastq.gz
# Pfam-A v32
pfam_db: /ebio/abt2_projects/ag-swart-loxodes/db/pfam/Pfam-A.hmm