compare short reads against htgs, nt, and wgs databases megablast_wrapper.py --db_build="$source_select" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff --eval_cutoff=$evalue_cutoff --filter_query=$filter_query --index_dir=${GALAXY_DATA_INDEX_DIR} --output=$output1 28 16 Yes No megablast

.. class:: warningmark **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. ----- **What it does** This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues. ----- **Output format** Output of this tool contains 13 columns delimited by Tabs: 1. Id of your sequence 2. GI of the database hit 3. Length of the database hit 4. % identity 5. Alignment length 6. # mismatches 7. # gaps 8. Start position in your sequence 9. End position in your sequence 10. Start position in database hit 11. End position in database hit 12. E-value 13. Bit score ------- **Reference** Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.