-D STR

Prefix name for reference index [*.index]. See APPENDIX How to build the reference index

-a STR

Query file, for SE reads alignment or one end of PE reads

-b STR

Query b file, one end of PE reads

-o STR

Output file for alignment results

-2 STR

Output file contains mapped but unpaired reads when do PE alignment

-u STR

Output file for unmapped reads, [none]

-m INT

Minimal insert size INT allowed for PE, [400]

-x INT

Maximal insert size INT allowed for PE, [600]

-n INT

Filter low quality reads containing more INT bp Ns, [5]

-t

Output reads id instead reads name, [none]

-r INT

How to report repeat hits, 0=none; 1=random one; 2=all, [1]

-R

RF alignment for long insert size(>= 2k bps) PE data, [none] FR alignment

-l INT

For long reads with high error rate at 3'-end, those can't align whole length, then first align 5' INT bp subsequence as a seed, [256] use whole length of the read

-s INT

minimal alignment length (for soft clip)

-v INT

Totally allowed mismatches in one read, when use subsequence as a seed, [5]

-g INT

Allow gap size in one read, [0]

-M INT

Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]

-p INT Multithreads, n threads, [1]

2bwt-builder <reference.fasta>

NOTE: 1. the reference input should only be FASTA format; 2. the program wil auto generate the index files in the directory where the fasta file is located, so confirm the permission at first.

1.8Gb RAM (for a genome as large as human's)

2.at least 8Gb hard disk to store index (for a genome as large as human's)

Linux x86_64