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```mermaid
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graph TD
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A[Raw data]-->|Cutadapt| B[Pre-cleaned data]
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B-->|Sickle| C[Cleaned data]
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C-->|BWA mem| D[Aligned reads against human genome]
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B-->|BWA mem| D[Aligned reads against human genome]
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D-->|Samtools view| E[.bam : only non-human reads]
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E-->|bamToFastq| F[New filtered .fastq files]
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F-->|gzip| G[Compressed .fastq files]
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G-->|Metaspades| H[Assembled reads]
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G-->|Megahit| H[Assembled reads]
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H-->|Prokka| I[Annotated reads]
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I-->|CD-HIT| J[Individual clustering]
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J-->|cd-hit_produce_table_clstr.py| J2[Link between representative cluster and members]
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J-->|CD-HIT| K[Global clustering]
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K-->|Join tables| L[Link initial proteins and final proteins]
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L-->|gffread| M[Contigs : gff transformed to gtf]
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M-->|bwa index| N[Indexation contig file]
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N-->|bwa mem| O[Aligned reads]
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O-->|Samtools view \nSamtools sort \nSamtools index| P[.bam file]
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P-->|featureCounts| Q[Transcript expression quantification]
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L-->|fasta_extract.pl| R[Transcripts]
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R-->|bwa index| S[Indexation transcript file]
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S-->|bwa mem| T[Aligned reads]
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T-->|Samtools view \nSamtools sort \nSamtools index| U[.bam file]
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U-->|Samtools idxstats| Q[Transcript expression quantification]
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A-->|FastQC| W[Quality control]
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B-->|FastQC| X[Quality control]
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C-->|FastQC| Y[Quality control]
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G-->|FastQC| Z[Quality control]
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W-->|MultiQC| AA[Quality control file]
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X-->|MultiQC| AA[Quality control file]
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Y-->|MultiQC| AA[Quality control file]
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Z-->|MultiQC| AA[Quality control file]
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Q-->|Python program| AB[Transcript quantification synthesis]
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AC[Database index Kaiju]-->|kaiju MEM| AD[Taxonomic classification of reads]
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G-->|kaiju MEM| AD[Taxonomic classification of reads]
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AD-->|kaiju2krona| AE[Formatted files for krona generation]
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AE-->|ktImportText| AF[Krona]
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AD-->|kaijuReport| AG[Summary files]
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``` |