OmicPipelines

A collection of codes to run meta-omic analyses

Requirements

Python 2.7, Biopython, Networkx

PRICE assembler (http://derisilab.ucsf.edu/software/price/) set to PATH

BLAST (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) set to PATH

PhyML (https://code.google.com/p/phyml/) set to PATH

muscle (http://www.drive5.com/muscle/) set to PATH

Codes

FindSeeds.py

This code generates a seed file for TargetedAssembly.py

Useage: python FindSeeds.py --ref_file seed.fa --ref_type nucl --fwd [options]

Options:

-h, --help show this help message and exit

--ref_file=REF_FILE FASTA (nucleotide or protein) file of reference sequences

--ref_type=REF_TYPE Indicate whether reference file is a nucleotide (nucl) or protein (prot) file.

--fwd=FWD FASTA/Q file of the metagenome. For paired end reads, -fwd will indicate the file with forward reads and -rev indicate the reverse reads

--outFile=OUTFILE Name of the output file that will contain the seed sequences (FASTA format).

--rev=REV FASTA/Q file that contains the reverse reads of paired end sequencing

--n_threads=N_THREADS Number of threads to use [1]

--evalue=EVALUE evalue cut-off to use if --search Y [1e-5]

TargetedAssembly.py

A pipeline for performing targeted assembly. (Can be used without executing FindSeeds.py).

Useage: python TargetedAssembly.py --seed_file seed.fa --fwd metagenome.fa --insert_size=N --output_file=output.fasta [options]

Options:

-h, --help show this help message and exit

--seed_file=SEED_FILE FASTA (nucleotide or protein) file of sequences to target

--fwd=FWD FASTA/Q file of the metagenome. For paired end reads, -fwd will indicate the file with forward reads and -rev indicate the reverse reads

--insert_size=INSERT_SIZE Insert size (Required). If reads are single end (--fwd only), use the max sequence length

--output_file=PRICEOUT Name for output file. Must end in ".fasta"

--rev=REV FASTA/Q file that contains the reverse reads of paired end sequencing

--n_threads=N_THREADS Number of threads to use [1]

--mate=MATE Designate --mate=1 if --fwd and --rev are mate-paired (pointing away from one another) rather than paired-end (pointing towards one another)

PredictProteins.py

BuildTree.py

Acknowledgements

These pipelines use software developed by others. More information is available at their resective sites (see Requirements).