vqwdm/metagenomics

Scripts for metagenomics and next generation sequencing data analysis

Scripts for pretreatment of paired-end sequences for metagenomics

QC_PE.py a script for Quality Control (QC) of Illumina Paired-End (PE) Reads.

DR_PE.py a script for De-Replication of Paired-End (PE) Reads.

MG_PE.py a script for Overlapping/Merging Paired-End (PE) Reads.

The scripts were written and tested in python 2.7.3 and biopython 1.64

(1) QC_PE.py -h usage: QC_PE.py [-h] -f FORWARD_READS_FP -r REVERSE_READS_FP [-a MAX_AMBIG] [-L MIN_SEQ_LENGTH] [-q AVERAGE_QUALITY] [-F {33,64}] -o OUTPUT_PREFIX

a script for Quality Control (QC) of Illumina Paired-End (PE) Reads [email protected]

optional arguments: -h, --help show this help message and exit

-f FORWARD_READS_FP, --forward_reads_fp FORWARD_READS_FP
The file path of input forward reads in FASTQ format.

-r REVERSE_READS_FP, --reverse_reads_fp REVERSE_READS_FP
The file path of input reverse reads in FASTQ format.

-a MAX_AMBIG, --max_ambig MAX_AMBIG
maxmium number of ambiguous bases. Default: 3

-L MIN_SEQ_LENGTH, --min_seq_length MIN_SEQ_LENGTH
minimum sequence length (bp). Default: 50

-q AVERAGE_QUALITY, --average_quality AVERAGE_QUALITY
minimum average quality, Default: 20

-F {33,64}, --phred_format {33,64}
format of phred quality score, Default: 33

-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
The prefix of filtered fastq files.

(2) DR_PE.py -h usage: DR_PE.py [-h] -f FORWARD_READS_FP -r REVERSE_READS_FP [-n FIRST_N_BASES] -o OUTPUT_PREFIX

a script for De-Replication of Paired-End (PE) Reads [email protected]

optional arguments: -h, --help show this help message and exit

-f FORWARD_READS_FP, --forward_reads_fp FORWARD_READS_FP The file path of input forward reads in FASTQ format.

-r REVERSE_READS_FP, --reverse_reads_fp REVERSE_READS_FP The file path of input reverse reads in FASTQ format.

-n FIRST_N_BASES, --first_N_bases FIRST_N_BASES Remove all but a single representative of clusters of reads whose first [N] base pairs are identical. Default: 50, as recommended by MG-RAST.

-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX The prefix of de-replicated fastq files.

(3) MG_PE.py -h usage: MG_PE.py [-h] -f FORWARD_READS_FP -r REVERSE_READS_FP [-j MIN_OVERLAP_LEN] -o OUTPUT_PREFIX

a script for Overlapping Paired-End (PE) Reads [email protected]

optional arguments: -h, --help show this help message and exit

-f FORWARD_READS_FP, --forward_reads_fp FORWARD_READS_FP The file path of input forward reads in FASTQ format.

-r REVERSE_READS_FP, --reverse_reads_fp REVERSE_READS_FP The file path of input reverse reads in FASTQ format.

-j MIN_OVERLAP_LEN, --min_overlap_len MIN_OVERLAP_LEN the minimum length (bp) for PE reads overlapping. Default: 10

-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX The prefix of overlapped fasta file