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Software for predicting library complexity and genome coverage in high-throughput sequencing.
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README.md
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load_data_for_complexity.hpp updating for using htslib instead of samtools source Jul 24, 2019
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preseq.cpp updating for using htslib instead of samtools source Jul 24, 2019
to-mr.cpp Adding the to-mr program to replace bam2mr Jul 24, 2019

README.md

This is the README file for the preseq package. The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

UPDATES TO VERSION 2.0.3

A bug in defect mode was fixed and a rng seed was added to allow for reproducibility.

UPDATES TO VERSION 2.0.0

We have added a new module, bound_pop, to estimate a lower bound of the population sampled from. Interpolation is calculated by expectation rather than subsampling, dramatically improving the speed.

UPDATES TO VERSION 1.0.2

We have switched the dependency on the BamTools API to SAMTools, which we believe will be more convenient for most users of preseq. Minor bugs have been fixed, and algorithms have been refined to more accurately construct counts histograms and extrapolate the complexity curve. More options have been added to lc_extrap. c_curve and lc_extrap are now both under a single binary for easier use, and commands will now be written as preseq lc_extrap [OPTIONS] Furthermore, there are updates to the manual for any minor issues encountered when compiling the preseq binary.

We release an R package called preseqR along with the preseq. It makes the preseq available in the R statistical environment. The submodule preseqR contains all required source code to build the R package.

CONTACT INFORMATION:

Timothy Daley tdaley@stanford.edu http://smithlabresearch.org

SYSTEM REQUIREMENTS:

The preseq software will only run on 64-bit UNIX-like operating systems and was developed on Linux systems. The preseq software requires a fairly recent C++ compiler (i.e. it must include tr1 headers). preseq has been compiled and tested on Linux and Mac OS X operating systems using GCC v5.3 or greater.

INSTALLATION:

This should be easy: unpack the archive and change into the archive directory. Then type make all. The programs will be in the archive directory. These can be moved around, and also do not depend on any dynamic libraries, so they should simply work when executed. If the desired input is in .bam format, htslib is required. Type

make HAVE_HTSLIB=1 all

to make the programs.

The HTSLib library can be obtained here: http://www.htslib.org/download

INPUT FILE FORMAT:

Input files can be either in BED or BAM file format. The file should be sorted by chromosome, start position, strand position, and finally strand if in BED format. If the file is in BAM format, then the file should be sorted using bamtools or samtools sort.

USAGE EXAMPLES:

Each program included in this software package will print a list of options if executed without any command line arguments. Many of the programs use similar options (for example, output files are specified with '-o'). To predict the yield of a future experiment, use lc_extrap. For the most basic usage of lc_extrap to compute the expected yield, use the command:

preseq lc_extrap -o yield_estimates.txt input.bed

If the input file is in .bam format, use the command:

preseq lc_extrap -B -o yield_estimates.txt input.bam

The yield estimates will appear in yield_estimates.txt, and will be a column of future experiment sizes in TOTAL_READS, a column of the corresponding expected distinct reads in EXPECTED_DISTINCT, followed by two columns giving the corresponding confidence intervals.

To investigate the past yield of an experiment, use c_curve. For the most basic usage, use the command:

preseq c_curve -o estimates.txt input.bed

If the input file is in .bam format, use the command:

preseq c_curve -B -o estimates.txt input.bam

The estimates will appear in estimates.txt with two columns. The first column gives the total number of reads in a theoretically smaller experiment and the second gives the corresponding number of distinct reads.

HISTORY

preseq was originally developed by Timothy Daley and Andrew Smith at the University of Southern California.

LICENSE

The preseq software for estimating complexity Copyright (C) 2014-2019 Timothy Daley and Andrew D Smith and Chao Deng and the University of Southern California

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

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