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PAired-eND Assembler for DNA sequences

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


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:
	./ && ./configure && make && sudo make install

If you receive an error that is not found, try running:
	sudo ldconfig


Please consult the manual page by invoking
	man pandaseq

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


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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