assign threshold

07_assignation/Assign_sintax.sh

@@ -111,7 +111,7 @@ all_sample_sequences_sort_uppercase="${all_sample_sequences_sort/.fasta/.upperca
 awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $0}}' $all_sample_sequences_sort > $all_sample_sequences_sort_uppercase
 ## Taxonomic assignation
 all_sample_sequences_sintax_ann="${all_sample_sequences_sort/.fasta/.sintax_ann.csv}"
-$usearch -sintax $all_sample_sequences_sort_uppercase -db $refdb_dir -sintax_cutoff 0.8 -strand plus -tabbedout $all_sample_sequences_sintax_ann
+$usearch -sintax $all_sample_sequences_sort_uppercase -db $refdb_dir -sintax_cutoff 0.98 -strand plus -tabbedout $all_sample_sequences_sintax_ann
 ## convert usearch output to obifasta
 all_sample_sequences_sintax_ann_fas="${all_sample_sequences_sintax_ann/.csv/.fasta}"
 $container_python2 07_assignation/convert_assign_sintax_2_obifasta.py -f $all_sample_sequences_sort -s $all_sample_sequences_sintax_ann -o $all_sample_sequences_sintax_ann_fas

07_assignation/Assign_vsearch.sh

@@ -110,7 +110,7 @@ all_sample_sequences_sort="${all_sample_sequences_ann/.fasta/.sort.fasta}"
 $obisort -k count -r $all_sample_sequences_ann > $all_sample_sequences_sort
 # Taxonomic assignation
 all_sample_sequences_vsearch_tag="${all_sample_sequences_sort/.fasta/.tag.vsearch}"
-$vsearch --usearch_global $all_sample_sequences_sort --db $refdb_dir --notrunclabels --id 0.8 --fasta_width 0 --top_hits_only --blast6out $all_sample_sequences_vsearch_tag
+$vsearch --usearch_global $all_sample_sequences_sort --db $refdb_dir --notrunclabels --id 0.98 --fasta_width 0 --top_hits_only --blast6out $all_sample_sequences_vsearch_tag
 ## convert vsearch assignation file into obifasta
 all_sample_sequences_vsearch_tag_obifasta="${all_sample_sequences_vsearch_tag/.vsearch/.vsearch.fasta}"
 $container_python2 07_assignation/convert_assign_vsearch_2_obifasta.py -f $all_sample_sequences_sort -a $all_sample_sequences_vsearch_tag -o $all_sample_sequences_vsearch_tag_obifasta