Users can also access our "restful" web service via client-side scripts without using web brower. By doing this, users not only can automate single analysis but also can compose complex analysis pipelines.

Single metagenomic analysis

Currently we provide the following analyses through client-side scripting:

CategoryNameDescription
clusteringcd-hit-est?fast DNA clustering
cd-hit?protein clustering
h-cd-hit?hierarchical protein clustering
cd-hit-454?filtering 454 duplicate reads
rRNA predictionblastn_rRNA?rRNA prediction by blastn program
hmm_rRNA?rRNA prediction by hmmer 3.0 program
tRNA predictiontRNA?tRNA prediction by tRNAscan-SE program
orf predictionorf_finder?orf prediction by six-reading-frame technique
metagene?orf prediction by metagene program
fraggene_scan?orf prediction by fraggene_scan program
function annotationcog?protein function annotation by COG database
kog?protein function annotation by KOG database
prk?protein function annotation by NCBI PRK database
pfam?protein function annotation by pfam database
tigrfam?protein function annotation by tigrfam database
pathway annotationkegg?pathway annoation by KEGG database
sequence infofna_stat?statistics of DNA sequences including length and GC content
faa_stat?statistics of protein sequences including length
quality controlqc_filter_fastq?removing reads with low average quality for a read with fastq format
qc_filter_fasta_qual?removing reads with low average quality for a read with fasta+quality format
trimm?trimming the low-quality tail of illumina reads
filtering sequencefilter_human?filtering human sequences from reads
taxonomy binningrdp_binning?taxonomic binning by rdp classifier program
frhit_binning?taxonomic binning by frhit program
OTU findercd-hit-otu?OTU finder by cd-hit-otu program
format conversionfastq2fasta?converting fastq file to fasta file

For each single metagenomic analysis, user can call it by

./client_submit_job.pl input_fasta_file_name program_name output_name "[email]" "[parameter_set_1]" "[parameter_set_2]" [input_fasta_file_name2] [job_id]

where:
input_fasta_file_name=>the name of input file of reads (required)
program_name=>the name of program, e.g. cd-hit-est (required)
output_name=>the name of output, e.g. output.zip (required)
email=>email address of the user (optional)
parameter_set_1=>parameter set 1, used for almost all programs (optional)
parameter_set_2=>used only for cd-hit program (2 steps) (optional)
input_fasta_file_name2=>used only for qc_filter_fasta_qual (optional)
job_id=>job id of previous analysis(optional). If job_id is not empty, "input_fasta_file_name" must be output file name of previous analysis (e.g. "output.1" for "cd-hit-est" analysis). This parameter is mainly used for multiple metagenomic analyses

For each single analysis, we provide an example script line. You can see it in details by clicking the correponding "?" picture near analysis name in the above table.

Multiple metagenomic analyses

Users can compose a complicated metagenomic analysis comprised of several single analyses via script. Please see the following figure for an illustrative example. For the above figure, users can call Rammcap_submit_job.pl for multiple analyses:

./Rammcap_submit_job.pl input_fasta_file_name program_path
where
input_fasta_file_name=>the nanme of input file of reads (required)
program_path=>the path where client_submit_job.pl is (required)
Users can also modify Rammcap_submit_job.pl according to their specific requirements.

Download scripts and examples

1. Scripts: (a) client_submit_job.pl for single metagenomic analysis; (b) Rammcap_submit_job.pl for multiple metagenomic analyses.

2. Examples for single metagenomic analysis: for each analysis, users can download examples from our web site and modify it to be used for their own analysis.

3. Example for multiple metagenomic analyses: For complicated metagenomics analyses including several above-mentioned single analyses, we provide an example and users can modify it to be used for their own analysis.

Notes

1. "LWP" and "HTTP" Perl modules must be installed for running "Rammcap_submit_job.pl" and "client_submit_job.pl" scripts.

2. When "Rammcap_submit_job.pl" is called, you should provide the path of "client_submit_job.pl".