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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.