PANDASEQ-SAM is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. This version works on SAM/BAM formatted files.
A working version of PANDAseq and libhts must first be installed, including the development headers.
On Ubuntu, this can be installed via
sudo apt-get install libhts-dev pandaseq-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 libpandaseq-sam.so.0 is not found, try running:
sudo ldconfig
If you have problems locating htslib/sam.h on newer version of MacOS, try running:
./autogen.sh && CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure && make && sudo make install
Please consult the manual page by invoking
man pandaseq-sam
though this is only summarises the differences. Consult
man pandaseq
for the details.
The short version is
pandaseq-sam -f seq.sam
or
pandaseq-sam -b -f seq.bam