ubwt: Uni-path BWT utilities

Installation

• OS: ubwt currently can only be complied and run on Linux/Unix.

• Dependency: zlib

• Toy example of test data are in test_data

git clone https://github.com/yangao07/ubwt.git
cd ubwt; make

Get started with test data in test_data

$ ./ubwt unipath ./test_data/chr20.ubwt -o ./test_data/chr20.unipath.fa
$ ./ubwt unipath ./test_data/chr20.ubwt -e ./test_data/chr20.edges -k 55 -a G -o ./chr20.unipath.gfa
$ ./ubwt index ./test_data/chr20.ubwt
$ ./ubwt query ./test_data/chr20.ubwt ./test_data/in.query

Commands and options

Program: ubwt
Usage:   ubwt <command> [options]

Commands: 
         unipath     generate uni-path sequence from BWT string
         index       build BWT index for uni-path sequence
         query       find exact match of query sequence with BWT index

Generate uni-path sequence from BWT string

Usage:    ubwt unipath [option] <BWT-STR>

Options:

    -t    [INT] Number of threads. [1]
    -f    [STR] Format of input bwt-str. [B]
                  "B": binary file, 4-bit per bp, 0/1/2/3/4:A/C/G/T/#(first 64-bit: length).
                  "P": plain text.
    -e    [STR] Edge sequence file in binary format. Required when output GFA format. [NULL]
    -k    [INT] Length of k-mer. Required when output GFA format.
    -a    [STR] Format of output file. [F]
                  "F": FASTA format.
                  "G": GFA format.
    -o    [STR] Output file. [stdout]

Example:

# FASTA output
$ ./ubwt unipath ./test_data/chr20.ubwt -o ./test_data/chr20.unipath.fa
$ head -n4 ./test_data/chr20.unipath.fa
>1_246
GGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCTGGGCGTCATGGCGGGCGCCTGTAGTCCCAGCTACCTGGGAGGTTGAGGTGGGAGAATCGCTTGAACCCGGGAGGCGGAGGCTGCAGCAGCTGAGATTGTGCCACTGCACTCCAGCCTTGGCCACAGAGCAAGACCTTGTCTCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATAT
>2_55
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATATATATATATA

# GFA output
$ ./ubwt unipath ./test_data/chr20.ubwt -e ./test_data/chr20.edges -k 55 -o ./test_data/chr20.unipath.gfa -a G
$ head -n4 ./test_data/chr20.unipath.gfa
S	1	GGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCTGGGCGTCATGGCGGGCGCCTGTAGTCCCAGCTACCTGGGAGGTTGAGGTGGGAGAATCGCTTGAACCCGGGAGGCGGAGGCTGCAGCAGCTGAGATTGTGCCACTGCACTCCAGCCTTGGCCACAGAGCAAGACCTTGTCTCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATAT	LN:i:246
L	1	+	6	+	54M
S	2	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATATATATATATATATATA	LN:i:55
L	2	+	3	+	54M

FASTA output format:

>uniID_uniLen
uniSeq

• uniID: ID of unipath
• uniLen: Length of unipath
• uniSeq: Sequence of unipath

GFA output format:

S   uniID   uniSeq  LN:i:uniLen
L   uniID1  +   uniID2  +   xxxM

• uniID: ID of unipath
• uniSeq: Sequence of unipath
• uniLen: Length of unipath
• xxx: k-1

Build BWT index for uni-path sequences

Usage:   ubwt index [option] <BWT-STR>

Options:

    -t    [INT] Number of threads. [1].
    -f    [STR] Format of input bwt-str. [B]
                  "B": binary file, 4-bit per bp, 0/1/2/3/4:A/C/G/T/#(first 64-bit: length).
                  "P": plain text.
    -o    [STR] Prefix of bwt-index file. [<BWT-STR>]

Example

$ ./ubwt index -t2 ./test_data/chr20.ubwt

• Output index file will have .ubwti suffix, For example, ./test_data/chr20.ubwt.ubwti

Find exact match of query sequence on BWT index

Usage: ubwt query <BWT-index.prefix> <in-query> > match.out

       Find exact match of input query on BWT-index.
       Return <unipath name> and <offset(1-based)> on unipath.

Example

$ ./ubwt query ./test_data/chr20.ubwt ./test_data/in.query
$ 9_661	11

• Output consists two columns: <unipath_name> <offset(1-based)>