User guide¶
Quick start¶
ACEPipe is installed in ACE HPC clusters. To activate ACEPipe:
$ source activate acepipe
To get the help or available tools in ACEPipe:
$ acepipe -h
$ acepipe --help
Which will return the available commands available:
Usage: acepipe [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
Commands:
makedb
runpipe
runqc
runsingle
To get further options available in the command:
$ acepipe runpipe -h
$ acepipe runpipe --help
Which will return all options available for the command:
Usage: acepipe runpipe [OPTIONS]
Options:
-h, --help Show this message and exit.
-s, --sheetfile TEXT provide sheetfile location
default=samplesheet.tab
-o, --outdir TEXT provide output folder location
default=acepipe_results
-e, --email TEXT provide email id
-dt, --taxonomydb TEXT provide reference taxonomy database location
example:
/usr/local/qiime_db/silva_taxonomy_db.qza
default=silvadb & unitedb
-dg, --genomedb TEXT provide reference sequence database location
example: /usr/local/qiime_db/silva_seq_db.qz
default=silvadb & unitedb
-qm, --qiimemode [forward|both]
provide qiime reads mode
default=forward
-l, --readlength INTEGER provide reads length to keep after trimming
default=250
-q, --quality INTEGER provide quality score threshold value
default=15
-j, --joblist TEXT provide job id as a comma-separated list
default=all
Input¶
Input file for ACEPipe is the samplesheet file which is generated by ACE LIMS and provided by the ACE Sequencing Team. Samplesheet is a tab delimited file which contains some information such as:
- Sample_ID
- Sample_Name
- Sample_Plate
- Sample_Well
- I7_Index_ID
- index
- I5_Index_ID
- index2
- Sample_Project
- Description
- Read 1 File
- Read 2 File
- Fwd_Primer_Name
- Fwd_Primer_TS_seq
- Rev_Primer_Name
- Rev_Primer_TS_seq
- Client_Sample_Name
ACEPipe expects the filename should shart with sample id. If your file name starts with job id, please rename the files.
The fastq file name format is CasavaOneEightSingleLanePerSampleDirFmt which naming is as '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'.
So the name of your files should be as: SAMPLEID_JOBID_OTHERID_L001_R1_001.fastq.gz.
Example: SB2658_J1235_S352_L001_R1_001.fastq.gz and SB2658_J1235_S352_L001_R2_001.fastq.gz
Output¶
ACEPipe wraps all the files with a html file. Transfer the result folder to your local computer and
open the index.html file in any internet browser (Google Chrome preferred).
Examples¶
To activate ACEPipe:
$ source activate acepipe
Example-1: Forward reads processing in QIIME2¶
To process only the forwards reads in QIIME2:
$ nohup acepipe runpipe -s samplesheet.tab -o output_folder -e id@eaxmple.com > acepipe_forward_output.log &
Example-2: Both reads processing in QIIME2¶
To process both reads in QIIME2:
$ nohup acepipe runpipe -s samplesheet.tab -o output_folder -qm both -e id@eaxmple.com > acepipe_both_output.log &
Example-3: Customized database¶
To create customized database:
$ acepipe makedb -dg location/to/reference/sequences/file -dt location/to/taxonomy/file -o output/to/custom/database
To use the customized database:
$ nohup acepipe runpipe -s samplesheet.tab -dg location/to/reference/sequences/file -dt location/to/taxonomy/file
-o output_folder > acepipe_forward_customDB_output.log &
Example-4: Customized quality control¶
To process with q value of 25 and reads length of 220:
$ nohup acepipe runpipe -s samplesheet.tab -o output_folder -q 25 -l 220 -e id@eaxmple.com > acepipe_forward_customQC_output.log &
Example-5: Single or multiple jobs processing¶
ACEPipe processes all jobs by default. However, a single job or multipe jobs can be processed. To process a single job:
$ nohup acepipe runpipe -s samplesheet.tab -o output_folder -J JOBID -e id@eaxmple.com > acepipe_forward_JOBID_output.log &
To process multiple jobs:
$ nohup acepipe runpipe -s samplesheet.tab -o output_folder -J JOBID1,JOBID2,JOBID3,JOBIDX -e id@eaxmple.com > acepipe_forward_JOBS_output.log &
Example-6: Single reads¶
To use only single reads:
$ nohup acepipe runsingle -s samplesheet.tab -o output_folder -rd forward > acepipe_single_forward_output.log &
Note
Please provide your valuable comments and suggestions to make ACEPipe better. If you need further help, please contact Dr. Shihab Hasan (shihab.hasan@uq.net.au).