Selected scripts and codes used in the dectection of Cyclospora cayetanensis from 18S and COX3 amplicon sequencing. Test data sets included in this repository are from a subset of samples pulled from COX3 sequencing.
Blast-NCBI-nt.sh use ncbi-blast+ with fasta files to blast against a selected database with a 90% ID & coverage cutoff and return results with tab-delimited format and the following parameters: queryID accession taxID title length percentID query coverage mismatch gapopen query start query end subject start subject end evalue bitscore.
samtools-extract-coordinates.sh extract bam alignments based on genome coordinates from indexed bam files. Requires two coordinates. Test with Test_dataset_GENESLICE.
Example Usage:
sh samtools-extract-coordinates.sh "NW_020312409:1749-1750" "NW_020312409:1874-1875"
samtools-ampliconclip.sh trim overhangs from extracted bam alignments. Requires bed file with designated trimming locations. Test with Test_dataset_GENESLICE following coordinate extraction.
Example Usage:
sh samtools-ampliconclip.sh 1749-1875-bed
Parse_Blast_Dict_dupcounts.py parse blast outputs and duplicate sequence count data from seqkit rmdup (https://github.com/shenwei356/seqkit) and return table with combined top counts based on max bitscores for all samples. A randomly selected hit will be selected if max bitscores are tied among several hits. Note: tied hits may include all hits with the same taxID, does not distinguish. Requires a blast output file and count data for each sample. Use with Test_dataset_BLAST.
An optional taxa -target may also be selected to retrieve all max bitscore hits based on taxa ID. Note: for target option, tied hits are only considered tied maxscore hits between different taxID (i.e tied hits among same taxID will considered unique and not tied). ** Warning: inconsistent counts may occur when using the string option if taxa have different names or are missing labels for the same taxID! **
General Parameters:
-d directory containing files
-s1 file suffix for blast output results
-s2 file suffix for duplicate count files
-o prefix for output files (optional)
-target character string or taxID (optional)
Example Usage:
python Parse_Blast_Dict_dupcounts.py -d . -s1 _blast-hits-nt.txt -s2 _duplicated.detail.txt
Example Usage with Targets:
python Parse_Blast_Dict_dupcounts.py -d . -s1 _blast-hits-nt.txt -s2 _duplicated.detail.txt -o Cyclo_ -target 88456
python Parse_Blast_Dict_dupcounts.py -d . -s1 _blast-hits-nt.txt -s2 _duplicated.detail.txt -o Eimeria_ -target Eimeria
FastqList.py create a list of representative sequence IDs for each sample based on a community percent threshold. Use with Test_dataset_FASTQLIST.
Parameters:
-d directory containing files
-s file suffix of duplicate count files
-p threshold percentage (given as a decimal)
Example Usage:
python FastqList.py -d . -s _duplicated.detail.txt -p 0.25
18S_Dendrogram.md rmarkdown to create dendrogram plot of most abundant taxa found in pond and sludge samples based on 18S gene sliced reads mapped to C. cayetanensis 18S gene region (655-807bp).