1. implement the simplest FM-index using just basic data structures
2. implement FM-index using wavelet trees

git clone --recursive https://github.com/iborko/fmindex

• run make
• executables will be located in bin folder (bin/fmindex, bin/test)

Binary will be located in bin folder (fmindex). Usage:
    fmindex <sequence> <reads> [<occurrence_table> [<bucket_size>]]

• <sequence> - path to the sequence on which the search will be made, FASTA format
• <reads> - path to the reads that will be searched, FASTQ format
• <occurrence_table> - can be 0 (matrix occurrence table), 1 (wavelet tree based occurrence table)
• <bucket_size> - bucket size for bit string rank in wavelet tree, optional, default is 20

Example:
    fmindex Esch_coli_536.fna Esch_coli_536_reads.fq 1 40

For every read from <reads> program generates two lines. First line is the FASTQ header and the second line is the list of all position indices of the current read in <sequence>. Indices are splitted with whitespaces.

Script test_run.sh can be used to run program on one of the example sequence. Example sequences are located in the test_data folder.

Example of run:
    test_run.sh test_data/Esch_coli_536.fna
This script will generate sets of (1000, 5000, 10000, 50000, 100000, 500000, 1000000) reads and run the fmindex on them, measuring CPU time and memory using time program.

1 Jochen Singer: A Wavelet Tree Based FM-Index for Biological Sequences in SeqAn, link