fastx_barcode_splitter.pl - FASTX Barcode Splitter
Barcode Splitter, by Assaf Gordon (firstname.lastname@example.org), 11sep2008
This program reads FASTA/FASTQ file and splits it into several smaller files,
Based on barcode matching. FASTA/FASTQ data is read from STDIN (format is
auto-detected.) Output files will be writen to disk. Summary will be printed
usage: r.pl --bcfile
PREFIX [--suffix SUFFIX]
- [--mismatches N] [--exact] [--partial N] [--help] [--quiet]
FILE - Barcodes file name. (see explanation below.)
PREFIX - File prefix. will be added to the output files. Can
- to specify output directories.
SUFFIX - File suffix (optional). Can be used to specify file
- Try to match barcodes at the BEGINNING of sequences.
- (What biologists would call the 5' end, and programmers
would call index 0.)
- Try to match barcodes at the END of sequences.
- (What biologists would call the 3' end, and programmers
would call the end of the string.) NOTE: one of --bol, --eol
must be specified, but not both.
N - Max. number of mismatches allowed. default is 1.
- Same as '--mismatches 0'. If both --exact
- are specified, '--exact' takes precedence.
N - Allow partial overlap of barcodes. (see explanation below.)
- (Default is not partial matching)
- Don't print counts and summary at the end of the run.
- (Default is to print.)
- Print lots of useless debug information to STDERR.
- This helpful help screen.
Example (Assuming 's_2_100.txt' is a FASTQ file, 'mybarcodes.txt' is the
- $ cat s_2_100.txt | fastx_barcode_splitter.pl --bcfile
mybarcodes.txt --bol --mismatches 2 \
/tmp/bla_ --suffix ".txt"
Barcode file format -------------------
Barcode files are simple text
files. Each line should contain an identifier (descriptive name for the
barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
- #This line is a comment (starts with a 'number' sign) BC1
GATCT BC2 ATCGT BC3 GTGAT BC4 TGTCT
For each barcode, a new FASTQ file will be created (with the barcode's
identifier as part of the file name). Sequences matching the barcode will be
stored in the appropriate file.
Running the above example (assuming "mybarcodes.txt" contains the
above barcodes), will create the following files:
- /tmp/bla_BC1.txt /tmp/bla_BC2.txt
The 'unmatched' file will contain all sequences that didn't match any barcode.
Barcode matching ----------------
** Without partial matching:
Count mismatches between the FASTA/Q sequences and the barcodes. The barcode
which matched with the lowest mismatches count (providing the count is small
or equal to '--mismatches N') 'gets' the sequences.
Example (using the above barcodes): Input Sequence:
- GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG GATCT (1 mismatch,
BC1) ATCGT (4 mismatches, BC2) GTGAT (3 mismatches, BC3) TGTCT (3
This sequence will be classified as 'BC1' (it has the lowest mismatch count). If
'--exact' or '--mismatches 0' were specified, this sequence would be
classified as 'unmatched' (because, although BC1 had the lowest mismatch
count, it is above the maximum allowed mismatches).
Matching with '--eol' (end of line) does the same, but from the other side of
** With partial matching (very similar to indels):
Same as above, with the following addition: barcodes are also checked for
partial overlap (number of allowed non-overlapping bases is '--partial N').
Example: Input sequence is ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG (Same as above,
but note the missing 'G' at the beginning.)
- ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG GATCT (4
- GATCT (1 mismatch)
Note: scoring counts a missing base as a mismatch, so the final mismatch count
is 2 (1 'real' mismatch, 1 'missing base' mismatch). If running with
'--mismatches 2' (meaning allowing upto 2 mismatches) - this seqeunce will be
classified as BC1.
The quality of this automatically generated manpage might be insufficient. It is
suggested to visit
to get a better layout as well as an overview about connected FASTX tools.