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Files:
Steps to operate the pipeline.docx : Manual
DatasetA:
1. A_demultfile.csv : Demultiplexing file for DatasetA
2. A_N055.fasta: Complete fasta file for DatasetA
3. A_N055.fastq: Complete fastq file for DatasetA
4. DatasetA_Sanger_references.fas: Sanger references for DatasetA
5. 1_A_MAFFT_barcode_all_nt_megablast: megablast output of MAFFT barcodes used for amino acid correction
6. 1_A_MAFFT_barcode_all_nt_megablast.fasta: Accession fasta retrieved from 1_A_MAFFT_barcode_all_nt_megablast
DatasetB:
1. B_demultfile.csv: Demultiplexing file for DatasetA
2. B_N052.fasta: Complete fasta file for DatasetB
3. B_N052.fastq: Complete fastq file for DatasetB
4. REFERENCE_B_f.fasta: Illumina references for DatasetB, end1
5. REFERENCE_B_r.fasta: Illumina references for DatasetB, end2
6. 1_B_MAFFT_barcode_all_nt_megablast: megablast output of MAFFT barcodes used for amino acid correction
7. 1_B_MAFFT_barcode_all_nt_megablast.fasta: Accession fasta retrieved from 1_B_MAFFT_barcode_all_nt_megablast
DatasetC:
C_demultfile.csv: Demultiplexing file for DatasetC
C_N030.fasta: Complete fasta file for DatasetC
C_N030.fastq: Complete fastq file for DatasetB
DatasetC_References_illumina.fasta: Illumina references for DatasetC
1_C_MAFFT_barcode_all_nt_megablast: megablast output of MAFFT barcodes used for amino acid correction
1_C_MAFFT_barcode_all_nt_megablast.fasta: Accession fasta retrieved from 1_C_MAFFT_barcode_all_nt_megablast