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1_merge_pear.sh
1_merge_pear.sh
 
 
2a_preparing_tags_LCPI.pl
2a_preparing_tags_LCPI.pl
 
 
2b_demulti_dual_index_linked.sh
2b_demulti_dual_index_linked.sh
 
 
3_tag_primer_clipping_clean_derep.sh
3_tag_primer_clipping_clean_derep.sh
 
 
4_clustering_swarm_with_chim_filter.sh
4_clustering_swarm_with_chim_filter.sh
 
 
5_BLAST_options.sh
5_BLAST_options.sh
 
 
5_Blast_results_format.pl
5_Blast_results_format.pl
 
 
5_taxa_assignment_table.pl
5_taxa_assignment_table.pl
 
 
6a_OTU_contingency_table.py
6a_OTU_contingency_table.py
 
 
6a_build_OTU_table.sh
6a_build_OTU_table.sh
 
 
6b_filter_OTU_table.sh
6b_filter_OTU_table.sh
 
 
BOLD_download_refs.sh
BOLD_download_refs.sh
 
 
BOLD_lineage_primers_cut.sh
BOLD_lineage_primers_cut.sh
 
 
COI_Diet_otu_table.tar.gz
COI_Diet_otu_table.tar.gz
 
 
COI_NCBI_tax_assignment.tar.gz
COI_NCBI_tax_assignment.tar.gz
 
 
DB1_NCBI_download_refs.sh
DB1_NCBI_download_refs.sh
 
 
DB2_primers_cut.sh
DB2_primers_cut.sh
 
 
DB3_NCBI_lineage.sh
DB3_NCBI_lineage.sh
 
 
NCBI_lineage_dups.pl
NCBI_lineage_dups.pl
 
 
NCBI_lineage_edit.pl
NCBI_lineage_edit.pl
 
 
README.md
README.md
 
 
Streptophyta_trnL_NCBI.tar.gz
Streptophyta_trnL_NCBI.tar.gz
 
 
Tutorial_for_setting_up_the_METAPIPE_Workshop2021_environment.pdf
Tutorial_for_setting_up_the_METAPIPE_Workshop2021_environment.pdf
 
 
Tutorial_for_transfering_files_to_GCP.pdf
Tutorial_for_transfering_files_to_GCP.pdf
 
 
count_fastq_sequences.sh
count_fastq_sequences.sh
 
 
merge_paired_end.png
merge_paired_end.png
 
 
metadata_COI_Diet.txt
metadata_COI_Diet.txt
 
 
metapipe-Install_Setup.ipynb
metapipe-Install_Setup.ipynb
 
 
metapipe-r.ipynb
metapipe-r.ipynb
 
 
metapipe-run.ipynb
metapipe-run.ipynb
 
 
target_trnL.uniq.fasta
target_trnL.uniq.fasta
 
 
trnL_S1_L001_R1_001_sub.tar.gz
trnL_S1_L001_R1_001_sub.tar.gz
 
 
trnL_S1_L001_R2_001_sub.tar.gz
trnL_S1_L001_R2_001_sub.tar.gz
 
 
trnL_sub_metadata.txt
trnL_sub_metadata.txt
 
 
trnL_sub_tags.txt
trnL_sub_tags.txt
 
 
trnL_subsample.assembled.tar.gz
trnL_subsample.assembled.tar.gz
 
 

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