split_libraries_illumina.py – Script for processing raw Illumina Genome Analyzer II data.

Description:

Script for parsing, library splitting, and quality filtering of raw Illumina Genome Analyzer II data.

Usage: split_libraries_illumina.py [options]

Input Arguments:

Note

[REQUIRED]

-m, --mapping_fp

The mapping filepath

[OPTIONAL]

-5, --five_prime_read_fp

The 5’ read filepath [default: None]

-3, --three_prime_read_fp

The 3’ read filepath [default: None]

-o, --output_dir

Output directory [default: ./]

-u, --store_unassigned

Store seqs which can’t be assigned to samples because of unknown barcodes [default: False]

-q, --quality_threshold

Max base call error probability to consider high-quality (probability of base call being error, so values closer to 1 mean that the base call is more likely to be erroneous) [default: 1e-05]

-r, --max_bad_run_length

Max number of consecutive low quality base calls allowed before truncating a read [default: 1; the read is trucated at thesecond low quality call]

-p, --min_per_read_length

Min number of consecutive high quality base calls to includea read (per single end read) [default: 75]

-n, --sequence_max_n

Maximum number of N characters allowed in a sequence to retain it – this is applied after quality trimming, and is total over combined paired end reads if applicable [default: 0]

-s, --start_seq_id

Start seq_ids as ascending integers beginning with start_seq_id[default: 0]

--rev_comp_barcode

Reverse compliment barcodes before lookup[default: False]

--barcode_in_header

Barcode is in header line (rather than beginning of sequence)[default: False]

Output:

Parse paired-end read data (-5 and -3 provided), write output to s_1_seqs.fasta:

split_libraries_illumina.py -5 s_1_1_sequences.fasta -3 s_1_2_sequences.fasta -b barcode_map_6bp.txt

Parse 5’ read only (-5 only provided), write output to s_1_5prime_seqs.fasta:

split_libraries_illumina.py -5 s_1_1_sequences.fasta -b barcode_map_6bp.txt

Parse 3’ read only (-3 only provided), write output to s_1_3prime_seqs.fasta:

split_libraries_illumina.py -3 s_1_2_sequences.fasta -b barcode_map_6bp.txt

Parse multiple 5’ read only files (multiple -5 values provided), write output to s_1_5prime_seqs.fasta, s_2_5primer_seqs.fasta:

split_libraries_illumina.py -5 s_1_1_sequences.fasta,s_2_1_sequences.fasta -b barcode_map_6bp.txt