split_libraries_fastq.py – This script performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).

Description:

Usage: split_libraries_fastq.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --sequence_read_fps

The sequence read fastq files (comma-separated if more than one)

-b, --barcode_read_fps

The barcode read fastq files (comma-separated if more than one)

-o, --output_dir

Directory to store output files

-m, --mapping_fps

Metadata mapping files (comma-separated if more than one)

[OPTIONAL]

--retain_unassigned_reads

Retain sequences which don’t map to a barcode in the mapping file (sample ID will be “Unassigned”) [default: False]

-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 barcode reads before lookup [default: False]

--rev_comp_mapping_barcodes

Reverse compliment barcode in mapping before lookup (useful if barcodes in mapping file are reverse compliments of golay codes) [default: False]

--rev_comp

Reverse compliment sequence before writing to output file (useful for reverse-orientation reads) [default: False]

--last_bad_quality_char

The last character to be considered low quality (i.e., these character and those before it will be considered low quality base calls) [default: B]

--barcode_type

The type of barcode used. This can be an integer, e.g. for length 6 barcodes, or golay_12 for golay error-correcting barcodes. Error correction will only be applied for golay_12 barcodes. [default: golay_12]

--max_barcode_errors

Maximum number of errors in barcode [default: 1.5]

Output:

Demultiplex and quality filter two lanes of Illumina run results and write results to ./sl_out/.:

split_libraries_fastq.py -i s_7_2_sequence.txt,s_8_2_sequence.txt -b s_7_1_sequence.txt,s_8_1_sequence.txt -o ./sl_out/ -m lane7_map.txt,lane8_map.txt