SWIFR: Smith-Waterman Implementation for Full Read-identifaction.

SWIFR utilizes the Smith Waterman algorithm to align a set of query sequences against ngs reads

Manual

Read the Manual to learn about the command line parameters. The Alignment Strategy is also useful for understanding the alignment method.

Dependencies

• io_lib_wrapper - (provided in external/io_lib_wrapper )
• io_lib - available at SourceForge
• kseq.h - For reading Fasta files
• tclap - Command Line Parsing available at SourceForge

Installing io_lib

wget [link above] && tar -xvzf [io_lib-1.14.6.tar.gz]
./configure
make
make install

You may need to provide CCPFLAGS (additional directories to search for header) and CC (which compiler) variables to the configure:

./configure CPPFLAGS="-I /usr/local/include/" CC="gcc"

If LZMA is missing, you can install XZ utils with homebrew install xz.

Installing TCLAP

wget [link above] && tar -xvzf [tclap-1.2.1.tar.gz]
./configure
make
make install

compile swifr:

make

Example of how to run swifr

/path/to/bin/swifr -f reads.fastq -q query_seqs.fasta -p 20 -s 20 -m 1 -k 10,1