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axe - axe Documentation

Axe is a read de-multiplexer, useful in situations where sequence reads contain the
barcodes that uniquely distinguish samples. Axe uses a rapid and accurate algorithm based
on hamming mismatch tries to competitively match the prefix of a sequencing read against a
set of barcodes. Axe supports combinatorial barcoding schemes.

Contents:

AXE USAGE

NOTE:
For arcane reasons, the name of the axe binary changed to axe-demux with version 0.3.0.
Apologies for the inconvenience, this was required to make axe installable in Debian
and its derivatives. Command-line usage did not change.

Axe has several usage modes. The primary distinction is between the two alternate
barcoding schemes, single and combinatorial barcoding. Single barcode matching is used
when only the first read contains barcode sequences. Combinatorial barcoding is used when
both reads in a read pair contain independent (typically different) barcode sequences.

For concise reference, the command-line usage of axe-demux is reproduced below:

USAGE:
axe-demux [-mzc2pt] -b (-f [-r] | -i) (-F [-R] | -I)
axe-demux -h
axe-demux -v

OPTIONS:
-m, --mismatch Maximum hamming distance mismatch. [int, default 1]
-z, --ziplevel Gzip compression level, or 0 for plain text [int, default 0]
-c, --combinatorial Use combinatorial barcode matching. [flag, default OFF]
-p, --permissive Don't error on barcode mismatch confict, matching only
exactly for conficting barcodes. [flag, default OFF]
-2, --trim-r2 Trim barcode from R2 read as well as R1. [flag, default OFF]
-b, --barcodes Barcode file. See --help for example. [file]
-f, --fwd-in Input forward read. [file]
-F, --fwd-out Output forward read prefix. [file]
-r, --rev-in Input reverse read. [file]
-R, --rev-out Output reverse read prefix. [file]
-i, --ilfq-in Input interleaved paired reads. [file]
-I, --ilfq-out Output interleaved paired reads prefix. [file]
-t, --table-file Output a summary table of demultiplexing statistics to file. [file]
-h, --help Print this usage plus additional help.
-V, --version Print version string.
-v, --verbose Be more verbose. Additive, -vv is more vebose than -v.
-q, --quiet Be very quiet.

Inputs and Outputs
Regardless of read mode, three input and output schemes are supported: single-end reads,
paired reads (separate R1 and R2 files) and interleaved paired reads (one file, with R1
and R2 as consecutive reads). If single end reads are inputted, they must be output as
single end reads. If either paired or interleaved paired reads are read, they can be
output as either paired reads or interleaved paired reads. This applies to both
successfully de-multiplexed reads and reads that could not be de-multiplexed.

The -z flag can be used to specify that outputs should be compressed using gzip
compression. The -z flag takes an integer argument between 0 (the default) and 9, where 0
indicates plain text output (gzopen mode "wT"), and 1-9 indicate that the respective
compression level should be used, where 1 is fastest and 9 is most compact.

The output flags should be prefixes that are used to generate the output file name based
on the barcode's (or barcode pair's) ID. The names are generated as: prefix + _ + barcode
ID + _ + read number + .extension. The output file for reads that could not be
demultiplexed is prefix + _ + unknown + _ + read number + .extension. The read number is
omitted unless the paired read file scheme is used, and is "il" for interleaved output.
The extension is "fastq"; ".gz" is appended to the extension if the -z flag is used.

The corresponding CLI flags are:

· -f and -F: Single end or paired R1 file input and output respectively.

· -r and -R: Paired R2 file input and output.

· -i and -I: Interleaved paired input and output.

The barcode file
The barcode file is a tab-separated file with an optional header. It is mandatory, and is
always supplied using the -b command line flag. The exact format is dependent on barcoding
mode, and is described further in the sections below. If a header is present, the header
line must start with either Barcode or barcode, or it will be interpreted as a barcode
line, leading to a parsing error. Any line starting with ';' or '#' is ignored, allowing
comments to be added in line with barcodes. Please ensure that the software used to
produce the barcode uses ASCII encoding, and does not insert a Byte-order Mark (BoM) as
many text editors can silently use Unicode-based encoding schemes. I recommend the use of
LibreOffice Calc (part of a free and open source office suite) to generate barcode tables;
Microsoft Excel can also be used.

Mismatch level selection
Independent of barcode mode, the -m flag is used to select the maximum allowable hamming
distance between a read's prefix and a barcode to be considered as a match. As "mutated"
barcodes must be unique, a hamming distance of one is the default as typically barcodes
are designed to differ by a hamming distance of at least two. Optionally, (using the -p
flag), axe will allow selective mismatch levels, where, if clashes are observed, the
barcode will only be matched exactly. This allows one to process datasets with barcodes
that don't have a sufficiently high distance between them.

Single barcode mode
Single barcode mode is the default mode of operation. Barcodes are matched against read
one (hereafter the forward read), and the barcode is trimmed from only the forward read,
unless the -2 command line flag is given, in which case a prefix the same length as the
matched barcode is also trimmed from the second or reverse read. Note that sequence of
this second read is not checked before trimming.

In single barcode mode, the barcode file has two columns: Barcode and ID.

Combinatorial barcode mode
Combinatorial barcode mode is activated by giving the -c flag on the command line. Forward
read barcodes are matched against the forward read, and reverse read barcodes are matched
against the reverse read. The optimal barcodes are selected independently, and the barcode
pair is selected from these two barcodes. The respective barcodes are trimmed from both
reads; the -2 command line flag has no effect in combinatorial barcode mode.

In combinatorial barcode mode, the barcode file has three columns: Barcode1, Barcode2 and
ID. Individual barcodes can occur many times within the forward and reverse barcodes, but
barcode pairs must be unique combinations.

The Demultipexing Statistics File
The -t option allows the output of per-sample read counts to a tab-separated file. The
file will have a header describing its format, and includes a line for unbarcoded reads.

AXE'S MATCHING ALGORITHM

Axe uses an algorithm based on longest-prefix-in-trie matching to match a variable length
from the start of each read against a set of 'mutated' barcodes.

Hamming distance matching
While for most applications in high-throughput sequencing hamming distances are a
frowned-upon metric, it is typical for HTS read barcodes to be designed to tolerate a
certain level of hamming mismatches. Given these sequences are short and typically occur
at the 5' end of reads, insertions and deletions rarely need be considered, and the
increased rate of assignment of reads with many errors is offset by the risk of falsely
assigning barcodes to an incorrect sample. In any case, reads with more than 1-2
sequencing errors in their first several bases are likely to be poor quality, and will
simply be filtered out during downstream quality control.

Hamming mismatch tries
Typically, reads are matched to a set of barcodes by calculating the hamming distance
between the barcode, and the first l bases of a read for a barcode of length l. The
"correct" barcode is then selected by recording either the barcode with the lowest hamming
distance to the read (competitive matching) or by simply accepting the first barcode with
a hamming distance below a certain threshold. These approaches are both very
computationally expensive, and can have lower accuracy than the algorithm I propose.
Additionally, implementations of these methods rarely handle barcodes of differing length
and combinatorial barcoding well, if at all.

Central to Axe's algorithm is the concept of hamming-mismatch tries. A trie is a N-ary
tree for an N letter alphabet. In the case of high-throughput sequencing reads, we have
the alphabet AGCT, corresponding to the four nucleotides of DNA, plus N, used to represent
ambiguous base calls. Instead of matching each barcode to each read, we pre-calculate all
allowable sequences at each mismatch level, and store these in level-wise tries. For
example, to match to a hamming distance of 2, we create three tries: One containing all
barcodes, verbatim, and two tries where every sequence within a hamming distance of 1 and
2 of each barcode respectively. Hereafter, these tries are referred to as the 0, 1 and
2-mm tries, for a hamming distance (mismatch) of 0, 1 and 2. Then, we find the longest
prefix in each sequence read in the 0mm trie. If this prefix is not a valid leaf in the
0mm trie, we find the longest prefix in the 1mm trie, and so on for all tries in ascending
order. If no prefix of the read is a complete sequence in any trie, the read is assigned
to an "non-barcoded" output file.

This algorithm ensures optimal barcode matching in many ways, but is also extremely fast.
In situations with barcodes of differing length, we ensure that the longest acceptable
barcode at a given hamming distance is chosen; assuming that sequence is random after the
barcode, the probability of false assignments using this method is low. We also ensure
that short perfect matches are preferred to longer inexact matches, as we firstly only
consider barcodes with no error, then 1 error, and so on. This ensures that reads with
barcodes that are followed by random sequence that happens to inexactly match a longer
barcode in the set are not falsely assigned to this longer barcode.

The speed of this algorithm is largely due to the constant time matching algorithm with
respect to the number of barcodes to match. The time taken to match each read is
proportional instead to the length of the barcodes, as for a barcode of length l, at most
l + 1 trie level descents are required to find an entry in the trie. As this length is
more-or-less constant and small, the overall complexity of axe's algorithm is O(n) for n
reads, as opposed to O(nm) for n reads and m barcodes as is typical for traditional
matching algorithms

· genindex

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