PAired-eND Assembler for DNA sequences – SAM/BAM format support
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README.md

PANDASEQ-SAM

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.

INSTALLATION

Build Status

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

USAGE

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