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PAired-eND Assembler for DNA sequences

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README
PANDASEQ
========

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

INSTALLATION
------------

Binary packages are available for recent versions of MacOS and Linux. Installing from source is not too difficult.

Development packages for zlib and libbz2 are needed, as is a standard compiler environment. On Ubuntu, this can be installed via
	sudo apt-get install build-essentials libtool automake zlib1g-dev libbz2-dev
On MacOS, the Apple Developer tools and Fink must be installed, then
	sudo fink install bzip2-dev

After the support packages are installed, one should be able to do:
	./autogen.sh && ./configure && make && sudo make install

If you receive an error that libpanadaseq.so.0 is not found, try running:
	sudo ldconfig

USAGE
-----

Please consult the manual page by invoking
	man pandaseq

The short version is
	pandaseq -f forward.fastq -r reverse.fastq


FAQ
---

Q: Can I insist that PANDAseq only assembler perfect sequences?
A: No. The whole point is to fix sequences which are probably good. There is no quality setting that will acheive this effect. You could write a plug-in to examine `overlap_mismatches`, but this really does miss the point. Moreover, assuming that the sequencer is right in the overlap region and in the non-overlapping regions requires an unsound leap in statistics.

Q: Can PANDAseq use multiple core/threads?
A: Yes, but you shouldn't turn it on until you've checked you need it. In most cases, PANDAseq is IO-bound, not CPU-bound; therefore, adding more CPU capacity would have no effect. Try monitoring a running copy of PANDAseq with `top`; watch the CPU% for the PANDAseq process and the overall system CPU waiting time (`%wa` in the banner at the top). If waiting time is low and CPU% is very high, then multi-threading may increase speed. If the CPU waiting time is high, threading will simply not help.
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