Quorum has been tested on Linux with gcc 4.4 to gcc 4.7.
You should download the latest release distribution tar ball from the
releases section. If
compiling from the github tree code, you will need autoconf,
automake and yaggo. You can download yaggo from the
github release page and
copy the yaggo problem into your PATH.
Quorum requires Jellyfish to be installed.
For Quorum to compile pkg-config must find Jellyfish. The following command must pring "OK":
pkg-config --exists jellyfish-2.0 && echo OK
If not, set the variable PKG_CONFIG_PATH appropriately.
If installing from the github tree, first run autoreconf -fi. Then
install the usual way:
./configure --prefix=/path/where/to/install
make
make install
The last command may need to be run as root, if installing in a system directory.
Only one switch (-s) is required to run Quorum. This switch specify
the size of the Jellyfish hash and it must be large enough so that all
k-mers will fit into memory. With Illumina reads, a good estimate for
this size is:
(G + k * n) / 0.8
where G is the estimated genome size, k is the k-mer length (24 by default) and n is the number of reads. If the chosen size is too small, quorum will stop with the error message: "Failed: Increase the size parameter".
For example, for a bacteria with 2 million Illumina reads in files read1.fastq and read2.fastq, the command would be:
quorum -s 50M read1.fastq read2.fastq
The output corrected file is called by default quorum_corrected.fa.
#Output format
The correction made are appended to the header line in the fasta format. For example, the following 101 bases long read:
@1204
GACCGGGCATGGGCTGAGCCTGTTCGGGAAGCTGACGGAGCCGGAAGAGGCCGGGATCGACCCTTCCGCCCCGCCCGCCGACTGGGTCGACCGGCCGGGCG
is corrected to:
>1204 86:sub:T-C 91:3_trunc 62:5_trunc
CTTCCGCCCCGCCCGCCGACTGGGCCGAC
The coordinate system is 0-based in the original reads (like a C or Perl array). Here, at base 86 a substitution was made from T to C. The 5_trunc is the index of the first base (0 if not specified) and the 3_trunc is the index after the last base (read length if not specified). Hence, the length of the corrected reads is computed as 3_trunc - 5_trunc (29 in this example). The uncorrected and corrected reads align as follows:
0 62 86 91 101
| | | | |
GACCGGGCATGGGCTGAGCCTGTTCGGGAAGCTGACGGAGCCGGAAGAGGCCGGGATCGACCCTTCCGCCCCGCCCGCCGACTGGGTCGACCGGCCGGGCG
CTTCCGCCCCGCCCGCCGACTGGGCCGAC
Other useful switches include (see quorum --help for a short
description of all of them).
--threads NUMBER
Number of threads to use.
--kmer-len LENGTH
Length of k-mer to use. Defaults to 24. This is limited to 31.
--contaminant FILE
Pass in a fasta or fastq file of contaminant sequences. The error correction program will truncate any reads which contains a k-mer present in the contaminant sequences.
--prefix NAME
By default, all output file have the form quorum_*. This can be
changed with this switch.
--min-q-char ASCII
This is the ASCII value of the base of quality encoding. If not specified, it is auto-detected: the first 1,000 reads of the first file are read and the minimum quality value seen in these reads is used for min-q-char. An error is raised if this auto-detected base is not one of the standard value (33, 59 or 64).