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.. _split_libraries_fastq:
.. index:: split_libraries_fastq.py
*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).
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**Description:**
**Usage:** :file:`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
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