KmerGO is a user-friendly tool to identify the group-specific sequences on two groups of high throughput sequencing datasets. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered “group-specific” here. Furthermore, KmerGO can also be applied to capture trait-associated sequences for continuous-trait dataset.
KmerGO2 is almost 2x faster than KmerGO.
Github for KmerGO(v1.x.x) is here.
Please cite: Wang Y, Chen Q, Deng C, Zheng Y and Sun F (2020) KmerGO: A Tool to Identify Group-Specific Sequences With k-mers. Front. Microbiol. 11:2067. doi: 10.3389/fmicb.2020.02067
Download the Linux command version of KmerGO2(x86 64bit): download link.
Decompress the file and enter the software path.
Type these commands if you first use KmerGO2:
sudo chmod +x KmerGO2
sudo chmod +x ./bin/*
You can type ./KmerGO2 -h for help message.
We prepared some FASTA format files which are stored in "test_data/samples".
And trait files can be also found in folder "test_data".
Because of the small size of testing data, "k=25 MinValue=1" and other parameters as defaults are recommended.
CommandLine version of KmerGO2 supports END-TO-END mode(tool=all) and FOUR-TOOLS mode(tool=kmc3/union/filtering/cap3). The main running command is ./KmerGO2 <tool> with following options:
| option | required | description |
|---|---|---|
| -i | Yes | input files path |
| -o | Yes | output files path |
| -t | No | a csv file path of trait information (required when tool is filtering or all) |
| -e | No | temp files path (required when tool is kmc3 or all, default: ./) |
| -m | No | mode, 0-categorical, 1-continuous (default: 0) |
| -k | No | k-mer length (k from 14 to 256, default: 40) |
| -ci | No | minimal K-mer occurring times (default: 2) |
| -cs | No | maximal K-mer occurring times (default: 65535) |
| -n | No | number of processes (default: 24) |
| -assl | No | when mode = 0, logical features ASS value (default: 0.8) |
| -p | No | numeric(mode=0) or logical(mode=1) features rank sum test p threshold value (default: 0.01) |
| -assn | No | when mode = 0, numeric features logistic regression ASS value (default: 0.8) |
| -corr | No | when mode = 1, numeric features coefficient of association ρ threshold value (default: 0.8) |
Example: ./KmerGO2 all -k 25 -ci 1 -n 2 -i ./test_data/samples/ -t ./test_data/categorical\ trait\ information.csv
Categorical Trait
Example1:
id,trait
1.fasta,A
2.fasta,A
3.fasta,B
...
Example2:
id,trait
SRR1.fastq,Case
SRR2.fastq,Control
SRR3.fastq,Case
...
Continuous Trait
Example:
id,trait
SRR1.fasta,1.02
SRR2.fasta,2.35
SRR3.fasta,5.22
...
Templates can be also found in the folder "test_data".
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KmerGO2 must be called from its own directory now because otherwise it cannot find the bin/ directory. (refer to issue6)
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The directory path reference by -i must have ONLY the relevant .fasta (or .fastq) files in that directory and nothing else.
Thank meshpv for suggestions.
Please send bug reports, comments, or questions to here.
Last update: 2023-03-08