bin/

Binary executables go here, but some packages will be relegated to subdirectories to keep things neater and avoid name conflicts.

Note that the gcc-4.5 related executables are now installed here. To use the 4.5 compilers you will need to set up your library path to point to /campusdata/BME235/lib and /campusdata/BME235/lib64.

• pluck_scripts/: a set of Python scripts written by Kevin Karplus are in subdirectory
• rdb/: a set of Perl scripts for treating files with tab-separated columns like a relational database

• qseq2fastq: A python script to convert from Illumina qseq to fastq format. Will by default do quality score conversion from Phred 64 to 33 and change .'s to N's. It can also filter reads that do not pass the Illumina filter.
• fastq_fix: A python script to fix fastq files that were converted without converting Phred quality scores or changing .'s to N's.