metagenome~use-genbank-fasta-as-reference

metagenome analysis pipeline with a GenBank FASTA file

input_1:FASTQ(.gz)

input_1/test.fq

@AUAI9:00041:00048
GCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCTGGTATTCCGGGGAGCACGCCTGTTCGAGTGTCGTGAAATACCTCAAAGCCGGATGCTTTGTTGCTATCTTGGCTTGGACTTGGACTTTGCCGCGCATGACTTTATGGTTGTGGCGGCTGGTCTTAAATGCATTAGTCTGACCCATGATGTATCTTTGGTTCTACTCGGCGTGATAATTATGACCGCTGAGGACATCTGCTTTTGGGCGGATGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@AUAI9:00046:00039
TCCTCCGCTTATTGATATGCTTAAGTTCAGCGGGTAGCCCTACCTGATTTCAGATCAAAATTTTGAATGAGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@AUAI9:00049:00031
GCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATCCCGGGGGGCATGCCTGTTCGAGCGTCATTTCTACCATTCAAGCTTTGCTTGGTTTGGGTATTGTAGCACTTCTTAACCTGGAGTTTTACATATCTTAAATGTAGACGGCAGCAAGTATATTAGTTCTGAGCGTA

input_2:FAFSTA

input_2/ITS250-2500_subset.fa

>EU272526.1 'Aporospora terricola' (nom. ined.) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
TTGGAAGTTAAAAANTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAAA
CAACTAGGCCGTAACAAGCCTTGAACCCTTCTCTACGCGCACCTTTACCTTCTCCTTCGG
CGGGTCAGCGCCCGCCGTCGGAACCAACAAAACCCCCTTTTGCATCTAGCATACCACCCG
TTCCGATACAAAACACAATCGTTACAACTTTCAACAATGGATCTCTTGGCTCTGGCATCG
ATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGA
ATCTTTGAACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCAT
CTACACCCTCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCCGCCTCCGCGCGCGGACTCG
CCCCAAATCCATTGGCAGCGTCCCCTCGCCCCCCTCTCGCGCAGCACGAATGCGCATGAC
GAGGGAGCGGCTTTTGGGATCGCGACCCACCCCCAAGATGACCACCGTCTTTGACCTCGG

input_2/ITS250-2500_subset.fa.mod.fasta

>EU272526.1 'Aporospora terricola' (nom. ined.) 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
TTGGAAGTTAAAAANTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAAA
CAACTAGGCCGTAACAAGCCTTGAACCCTTCTCTACGCGCACCTTTACCTTCTCCTTCGG
CGGGTCAGCGCCCGCCGTCGGAACCAACAAAACCCCCTTTTGCATCTAGCATACCACCCG
TTCCGATACAAAACACAATCGTTACAACTTTCAACAATGGATCTCTTGGCTCTGGCATCG
ATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGA
ATCTTTGAACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCAT
CTACACCCTCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCCGCCTCCGCGCGCGGACTCG
CCCCAAATCCATTGGCAGCGTCCCCTCGCCCCCCTCTCGCGCAGCACGAATGCGCATGAC
GAGGGAGCGGCTTTTGGGATCGCGACCCACCCCCAAGATGACCACCGTCTTTGACCTCGG

input_3:*.accession2taxid.gz

Command

metagenome~use-genbank-fasta-as-reference -c 16 -a input_3/nucl_gb.accession2taxid.gz input_1/ input_2/ITS250-2500_subset.fa

Output

input_1/test.fasta.blast.filtered.name.lca.cnt2.input

id	test
root;cellular organisms;Eukaryota;Opisthokonta;Fungi	342
unknown	165
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetidae;Agaricales;Tricholomataceae;Tricholoma	113
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetes incertae sedis;Russulales;Russulaceae;Russula	104
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;unclassified Fungi;fungal sp.	43
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya	27
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Ascomycota;saccharomyceta;Pezizomycotina;leotiomyceta;Eurotiomycetes;Chaetothyriomycetidae	15
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Ascomycota;saccharomyceta;Pezizomycotina;leotiomyceta;dothideomyceta;Dothideomycetes;Dothideomycetes incertae sedis;Helicoon	14
root;cellular organisms;Eukaryota;Opisthokonta;Fungi;unclassified Fungi;fungal sp. 6 GM 15-19	12

input_1/test.fq.html

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