Usage of QC-Blind

Functions & Commands

  • classification


    $ sh classification.sh SAMPLE_NAME reads.fa

  • concoct


    $ sh concoct.sh SAMPLE_NAME contigs.fa PEreads1 PEreads2 species_number

  • reads mapping contigs 


    $ sh reads_mapping.sh SAMPLE_NAME contigs_cutting.fa PEreads1 PEreads2

  • find target_cluster


    $ sh target_find.sh contigs_cutting.fa marker.fa clustering_gt1000.csv SAMPLE_NAME

  • analysis clusters


    $ sh blast_megahit.sh contigs_cutting.fa blast_result_file clustering_gt1000.csv out.F DIR_NAME

  • evaluation


    $ sh target_evaluation.sh clusterN(target cluster) contig_species cluster_sN(target cluster) out.F DIR_NAME

  • dataloss


    $ sh dataloss.sh contigs_list clustering_gt1000.csv out.F DIR_NAME

  • extract target reads


    $ sh findclusterreads.sh cluster_sN(target cluster) out.F SAMPLE_NAME

  • coverage


    $ python coverage_percent.py


  • Tools used to make this:

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Huazhong University of Science & Technology

Information

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