Usage

For impatient users,

./squat.sh seq1 seq2 ... seqN
         -o <output_dir>  
         -r <genome_assembly> 

Please specify the path of the sequencing reads and the assembly to which they are mapped.

For paired-end reads, it is recommended to combine them into a single file. Otherwise, SQUAT also supports the input of multiple sequence files and generates multiple quality assessment reports in the same directory.

Primary output

SQUAT will generate an HTML index and a directory containing all the analysis information, both termed the same name as the sequencing reads file.

[output_dir]/[seq.html]

The table of content to link to other reports. (Index page)

[output_dir]/[seq]/[pre-assembly_report.html]

A pre-assembly report based on quality scores

[output_dir]/[seq]/[post-assembly_report.html]

A post-assembly report based on read mapping

If you need to re-generate the reports, execute gen_report.sh with the same arguments as squat.sh. This will save you much of the time. (Make sure to keep all the output files generated from squat.sh before execution) For details of the output directory structure, see output section.

Command Options

SQUAT runs from the command line with the following options:

-h (or --help)

Display the complete command options on screen.

-o < path >

The path to output directory.

-r < str >

Path to the assembly file as reference for alignment. SQUAT accepts FASTA format.

-g < path >

Assembly file. The tool accepts assemblies or reference genomes in FASTA format. (Remove contigs with all Ns before use)

-t < int > (or --thread < int >)

Number of threads to use. The default value is 1/3 of the number of CPUs of the current machine.

-f (or --flush)

Flush the sam file after each mapping experiment in {output_dir}/{seq}/{aligner}.

-s < str >

Return the subset of sequencing reads with labels specified in capitals. For ex., -s PSC means only selecting reads labeled with P, S, and C). The subset of sequencing reads will be stored in {output_dir}/{seq}/subset.

-g < str >

Path to the reference genome file for GAGE benchmark tool.

--gage

Activate gage mode for assembly evaluation, must specify reference genome (-g).

--sample-size < int >

Specify the read size for random sampling, default 1M

--all

Deactivate random sampling, take the whole read file as input.

-c < float >

Threshold for overall sequencing quality. Sequencing datasets whose percentage of poor quality reads exceeding the threshold will be determined poor quality and fail the assessment, default 0.2.

--mt < float > (or --mismatch_thre < float >)

Threshold for reads with substitution errors. Reads whose mismatch ratio exceeds the threshold will be determined poor quality, default 0.2.

--ct < float > (or --clip_thre < float >)

Threshold for reads containing clips. Reads whose clip ratio exceeds the threshold will be determined poor quality, default 0.3.

--ot < float > (or --others_thre < float >)

Threshold for reads with other errors. Reads whose error percentage exceeds the threshold will be determined poor quality, default 0.1

--nt < float > (or --n_thre < float >)

Threshold for reads containing N. Reads whose N ratio exceeds the threshold will be determined poor quality, default 0.1.

--seed < int >

The seed for random sampling, default 0.