|
|
```mermaid
|
|
|
graph TD
|
|
|
A[Raw data]-->B[Cutadapt]
|
|
|
B-->C[Sickle]
|
|
|
A-->D[FastQC]
|
|
|
B-->E[FastQC]
|
|
|
C-->F[FastQC]
|
|
|
B-->G[Alignment_filter]
|
|
|
C-->G[Alignment_filter]
|
|
|
G-->H[FastQC]
|
|
|
A[Raw data]-->B[cutadapt]
|
|
|
B-->C[sickle]
|
|
|
A-->D[fastqc_raw_reads]
|
|
|
B-->E[fastqc_cutadapt]
|
|
|
C-->F[fastqc_sickle]
|
|
|
B-->G[alignment_filter]
|
|
|
C-->G[alignment_filter]
|
|
|
G-->H[fastqc_after_alignment_filter]
|
|
|
I[index_db_kaiju]-->J[kaiju]
|
|
|
G-->J[kaiju]
|
|
|
G-->K[metaspades]
|
|
|
G-->L[megahit]
|
|
|
K-->M[prokka]
|
|
|
M-->N[individual_cd_hit]
|
|
|
N-->|cd_hit_produce_table_clstr.py|T[cd_hit_produce_table_clstr]
|
|
|
N-->O[global_cd_hit]
|
|
|
L-->M[prokka]
|
|
|
O-->|cd_hit_produce_table_clstr.py|P[cd_hit_produce_table_clstr]
|
|
|
P-->Q[Quantification]
|
|
|
D-->S[MultiQC]
|
|
|
E-->S[MultiQC]
|
|
|
F-->S[MultiQC]
|
|
|
H-->S[MultiQC]
|
|
|
T-->Q[Quantification]
|
|
|
K-->M[assembly_metrics]
|
|
|
L-->M[assembly_metrics]
|
|
|
K-->N[prokka]
|
|
|
L-->N[prokka]
|
|
|
N-->O[rename_contigs_genes]
|
|
|
O-->P[individual_cd_hit]
|
|
|
P-->|cd_hit_produce_table_clstr.py|Q[individual_cd_hit_produce_table_clstr]
|
|
|
P-->R[global_cd_hit]
|
|
|
R-->|cd_hit_produce_table_clstr.py|S[cd_hit_produce_table_clstr]
|
|
|
O-->T[Quantification]
|
|
|
G-->T[Quantification]
|
|
|
D-->U[multiqc]
|
|
|
E-->U[multiqc]
|
|
|
F-->U[multiqc]
|
|
|
H-->U[multiqc]
|
|
|
style A fill:#01d6ff
|
|
|
``` |
|
|
\ No newline at end of file |