GGMP-Regional variations
Introduction
Analysis pipeline for GGMP-Regional variations
Copyright
Copyright: Prof. Hong-Wei Zhou
Institution: State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China, 510282
Email: biodegradation@gmail.com
Author
Author: Hui-Min Zheng, Pan Li, Xian Wang and Yan He
Last update: 2018-02-08
Email: 328093402@qq.com
Index
1 Environment
1.1 System
1.1.1 System Platform
1.1.2 Hardware
1.2 Qiime
1.2.1 Qiime version
1.2.2 System information
1.2.3 QIIME default reference information
1.2.4 QIIME config values
1.3 BBMap
2 Data
2.1 original sequences
3 Scripts
3.1 Perl Scripts
4 Direction for use
4.1 Configuring the system environment files and variables
4.2 Location of the files
4.3 Run pipeline
5 How to get the data?
5.1 How to get the original sequences?
1 Environment
1.1 System
1.1.1 System Platform
Platform: Linux2
Version: Linux version 2.6.32-573.8.1.el6.x86_64 (mockbuild@c6b8.bsys.dev.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-16)(GCC))
OS: CentOS release 6.7 (Final)
1.1.2 Hardware
Cpu(s): >10
thread: >10
RAM: >10G
Hard disk: >2T
1.2 Qiime
1.2.1 Qiime version
Version: qiime 1.9.1
1.2.2 System information
Platform: Linux2
Python version: 2.7.10 (default, Dec 4 2015, 15:36:19) [GCC 4.4.7 20120313 (Red Hat 4.4.7-16)]
Python executable: /usr/local/bin/python
1.2.3 QIIME default reference information
For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
NumPy version: 1.11.0
SciPy version: 0.17.1
pandas version: 0.17.1
matplotlib version: 1.4.3
biom-format version: 2.1.5
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.51
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.00
swarm version: Swarm 1.2.19 [Dec 5 2015 16:48:11]
gdata: Installed.
1.2.4 QIIME config values
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html
http://qiime.org/tutorials/parallel_qiime.html
QIIME config values
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html
http://qiime.org/tutorials/parallel_qiime.html
blastmat_dir: None
pick_otus_reference_seqs_fp: /usr/local/lib/python2.7/sitepackages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
python_exe_fp: python
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: /usr/local/data/core_set_aligned.fasta.imputed
cluster_jobs_fp: None
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /usr/local/lib/python2.7/sitepackages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
qiime_test_data_dir: None
template_alignment_lanemask_fp: /usr/local/data/lanemask_in_1s_and_0s.txt
jobs_to_start: 1
slurm_time: None
cloud_environment: False
qiime_scripts_dir: /usr/local/bin
denoiser_min_per_core: 50
working_dir: None
assign_taxonomy_id_to_taxonomy_fp: /usr/local/lib/python2.7/sitepackages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 2
1.3 BBMap
BBTools bioinformatics tools, including BBMap.
Author: Brian Bushnell, Jon Rood
Language: Java
Version 36.32
2 Data
2.1 original sequences
format of sequences : fastq
Number of fq files: 36
fq_filenames: 1.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_1.fq
1.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_2.fq
1.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_1.fq
1.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_2.fq
1.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_1.fq
1.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_2.fq
1.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_1.fq
1.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_2.fq
2.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_1.fq
2.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_2.fq
2.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_1.fq
2.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_2.fq
2.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_1.fq
2.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_2.fq
2.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_1.fq
2.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_2.fq
3.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_1.fq
3.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_2.fq
3.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_1.fq
3.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_2.fq
3.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_1.fq
3.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_2.fq
3.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_1.fq
3.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_2.fq
4.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_1.fq
4.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_2.fq
4.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_1.fq
4.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_2.fq
4.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_1.fq
4.Clean_FCHVTWCBCXX_L1_wHAXPI034526-108_2.fq
4.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_1.fq
4.Clean_FCHVTWCBCXX_L2_wHAXPI034526-108_2.fq
5.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_1.fq
5.Clean_FCHVJVMBCXX_L1_wHAXPI034525-109_2.fq
5.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_1.fq
5.Clean_FCHVJVMBCXX_L2_wHAXPI034525-109_2.fq
3 Scripts
3.1 Perl Scripts
3.1.1 Preprocessing.pl
Function: Pipline of preprocessing, this script performs all processing steps through building the OTU table with several pair of fastq file.
Last updata: 2016-09-18
Author: Huimin Zheng
3.1.2 Illumina_pairend_preprocessing.pl
Function: This script performs all processing steps through building the OTU table with one pair of fastq file.
Location: Called by the pipeline--Preprocessing.pl
Last updata: 2016-08-08
Author: Yan He
3.1.3 trim_200bp.pl
Function: Trim the fastq file to 200bp, this can reduce the computational burden while using enough information to do overlapping
Location: Called by the script--Illumina_pairend_preprocessing.pl
Last updata: 2016-08-08
Author: Hua-Fang Sheng
3.1.4 pairend.extract_sequences.pl
Function: Do library splitting, as barcodes on both ends is not quite supported by QIIME at the moment (QIIME 1.9.1)
Location: Called by the script--Illumina_pairend_preprocessing.pl
Last updata: 2016-08-08
Author: Yan He
4 Direction for use
4.1 Configuring the system environment files and variables
Configuring the system environment files and variables based on the (1) Environment
4.2 Location of the files
put the scripts, bbmap folder and supplementary files in the same path
put all fastq files in the same path
4.3 Run pipeline
4.3.1 Preprocessing: From raw sequences to BIOM
perl Preprocessing.pl <fq_dir> <metadata.list> <threads> <output_dir>
<fq_dir>: Path to the folder containing all fastq files.
<metadata.list>: Path to file listing path to metadata file.
<threads>: Specify number of threads.
<output_dir>: The output directory.
# nohup perl Preprocessing.pl <fq_dir> <metadata.list> <threads> <output_dir> > Preprocessing.log 2>&1 &
5 How to get the data?
5.1 How to get the original sequences?
The 16S gene sequencing reads of GGMP have been deposited in EBI under accession PRJEB18535.