Metagenomic analysis workflow for the identification and quantification of antimicrobial resistance genes (ARG) from human stool samples. Authors = Zeya Xue, Yirui Tang, Danielle Lemay
Oliver A, Xue Z, Villanueva YT, Durbin-Johnson B, Alkan Z, Taft DH, Liu J, Korf I, Laugero KD, Stephensen CB, Mills DA, Kable ME, Lemay DG. Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults. mBio. 2022 Jun 28;13(3):e0010122. doi: 10.1128/mbio.00101-22. Epub 2022 May 10. PMID: 35536006; PMCID: PMC9239165. Link to the paper: https://pubmed.ncbi.nlm.nih.gov/35536006/
See the init/ folder for scripts that were used for dowloading and setting up software/databases.
https://bic-berkeley.github.io/psych-214-fall-2016/sys_path.html (read the "crude hack" part)
These python packages directly in the folder where the scripts are to help python look for the necessary packages.
numpy bin/ f2py, Python module numpy.f2py numpy numpy-1.16.6.dist-info
pytz pytzgit pytz-2019.3.dist-info
pandas pandas pandas-0.24.2.dist-info
six six-1.13.0.dist-info six.py six.pyc
dateutil
See the master_pipeline/ folder
"ARG_pipeline_v0.X.sh" is the master script containing the entire AMR pipeline, with preferred software/method/order of sequence processing.
Individual steps of the pipeline are in method_dev/ folder. Individual steps are labelled with their step number and procedure. For example, step1_BMTagger.sh is for the 1st step in the AMR pipeline that removes human DNA with BMTagger.
See the sequence_QC/ folder
+ hiseq_qc.sh: sequencing QC for two HiSeq runds
+ hts_SeqScreener_Phix.sh: find PhiX sequences
+ pipeline_stats.ipynb: Jupyter notebook to generate QC figures for raw and processed sequences
See the taxonomy/ folder
+ kraken2_struo95.sh: whole community taxonomy identification with Kracken2-Bracken pipeline
+ megahit_kraken_unmap.sh: troubleshooting script that assembles unmapped reads from Kraken2
+ metaphlan2.sh: whole community taxonomy identification with metaphlan2 method
See the utilties/ folder
+ checksums_bash.sh: check sums for downloaded sequence files to make sure files ware not corrupted
+ count_fasta_length.sh: calculate the length of fasta files
+ count_fq_length.sh: calculate the length of fastq files
+ count_fq.sh: count the number of reads in each fastq or fastq.gz file
+ discover_adapter_sequences.sh: find adapter sequences from fastq files
+ DNAtoAA_transcription_translation.py: transcribe DNA to amino acid sequences using the NCBI "11-bacterial" codon table
+ first_line2new_file.sh: this script takes the first line of each file in the the loop and writes the lines to a new file
+ gunzip_loop.sh: unzip all sequence files in a loop
+ human_ref_format4BMTagger.sh: format the human genome reference for BMTagger
+ make_RPKG_normtab.py: supportive script that normalize the ARG data table with MicrobeCensus
+ prefix_to_compline.py: converts partial headers extracted from sam file to full headers
+ subset_reads.sh: subset sequence files in a loop