README
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6
7....Paired-End reAd mergeR....
8
9Authors: Jiajie Zhang, Kassian Kobert, Tomas Flouri, Alexandros Stamatakis
10
11License: Creative Commons license
12 with
13Attribution-NonCommercial-ShareAlike 3.0 Unported
14
15Introduction:
16-------------
17PEAR assembles Illumina paired-end reads if the DNA fragment sizes are smaller
18than twice the length of reads. PEAR can assemble 95% of reads with 35-bp mean
19overlap with a false-positive rate of 0.004. PEAR also works with multiplexed
20data sets where the true underlying DNA fragment size varies. PEAR has an
21extremely low false-positive rate of 0.0003 on data sets where no overlap exists
22between the two reads (i.e. when DNA fragment sizes are larger than twice the
23read length).
24
25For more information, requests and bug-reports visit our website at
26
27 http://www.exelixis-lab.org/web/software/pear
28
29Requirements:
30-------------
31PEAR requires the autotools build system and libtool in order to proceed with
32the installation steps. In case you do not have autotools and libtool, you can
33install them using the command:
34
35sudo apt-get install build-essential autoconf automake libtool
36
37Additionally, if you would like to compile bzip2 and/or gzip support in PEAR,
38you will need to have bzlib and/or zlib installed on your system before
39installing PEAR. You can install them both with:
40
41sudo apt-get install libbz2-dev zlib1g-dev
42
43How to compile:
44---------------
451. git clone https://github.com/xflouris/PEAR.git
462. cd PEAR
473. ./autogen.sh
484. ./configure
495. make
506. sudo make install
51
52How to run self-tests:
53----------------------
541. Make sure you have python 2.4 (or newer) installed
552. Go to the "test" folder
563. type: ./test.py
57
58This will run PEAR on several simulated data sets with various options to check
59if the newly compiled program works properly.
60
61How to use:
62-----------
63PEAR can robustly assemble most of the data sets with default parameters. The
64basic command to run PEAR is
65
66 ./pear -f forward_read.fastq -r reverse_read.fastq -o output_prefix
67
68The forward_read file usually has "R1" in the name, and the reverse_read
69file usually has "R2" in the name.
70
71Output files:
72-------------
73PEAR produces 4 output files:
74
751. output_prefix.assembled.fastq - the assembled pairs
762. output_prefix.unassembled.forward.fastq - unassembled forward reads
773. output_prefix.unassembled.reverse.fastq - unassembled reverse reads
784. output_prefix.dicarded.fastq - reads which did not meet criteria specified in options
79
80Advanced usage:
81---------------
82
83For further options and fine-tuning type
84
85 ./pear -h
86
87Important information:
88----------------------
891. The input files must be in FASTQ format
902. PEAR does not check the paired-end reads names. PEAR assumes that the reads
91in both files are in the same flowcell position if they appear on the same line
92number. Therefore, the validity of the input files is left as a user
93responsibility.
94
95How to cite:
96------------
97J. Zhang, K. Kobert, T. Flouri, A. Stamatakis. PEAR: A fast and accurate Illumina
98Paired-End reAd mergeR. Bioinformatics 30(5): 614-620, 2014.
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100