Random Assembler - Micro genome assembler. Uses BWT for seeding/pattern matching and a greedy score based aligner.

random_assembler [-ms <match_score>] [-mp <mismatch_penalty>] [-gp <gap_penalty>] [-ep <extended_penalty>] [-vb] [-mascot] -irf <input_reference> -ird <input_reads> -m <allowed_mismatches> -t <num_threads>

Random Assembler is an ultrafast and memory-efficient tool for assebmling reads to long reference sequences.

-irf <input_reference> Specify the input reference file.

-ird <input_reads> Specify the input reads file.

-m <allowed_mismatches> Specify the allowed number of mismatches.

-t <num_threads> Specify the number of threads to be used.

-ms <match_score> Specify the match score. (Default: 1)

-mp <mismatch_penalty> Specify the mismatch penalty. (Default: 4)

-gp <gap_penalty> Specify the gap penalty. (Default: 6)

-ep <extended_penalty> Specify the extended penalty. (Default: 1)

-vb Enable verbose mode.

-mascot Print mascot.

This program, abraracourcix, was created by Christophe Khalil (cak29@mail.aub.edu) and Ali Chehab (amc33@mail.aub.edu) on 20/11/2023.

This program is licensed under the MIT License. If you use this program, please cite the authors.

Report bugs to cak29@mail.aub.edu and amc33@mail.aub.edu.

More information can be found in the report.pdf.

random_assebmler -irf reference.txt -ird reads.txt -m 2 -t 8 -vb

compile flags: -std=c++17 -fopenmp -O2

Assumptions:

• inputs are in text format and contain no symbols
• reads do not come with a quality score (no quality score provided)
• single stranded input