A command-line based tool to browse FastQC output. Written in Python 2.7.
python fastqc_browser.py -i fastq_output_dir/
FastQC-browser takes a single argument -i/--input-directory, which is a directory containing output from FastQC with a structure like the following tree:
-fastqc_output_dir/
|-- sample1/
|-- sample1_1.zip
|-- sample1_2.zip
|-- report.html
|-- sample2/
|-- sample2_1.zip
|-- sample2_2.zip
|-- report.html
|-- sample3/
|-- sample3_1.zip
|-- sample3_2.zip
|-- report.html
Supported commands are:
- help - Prints available commands
- exit - Quits the program
- open_sample_html_report - Open HTML report in browser (if available)
- print_global_stats - Prints total number of PASS/WARN/FAILs
- print_module_stats - Prints stats (PASS/WARN/FAIL) per module
- print_sample_details - Prints stats for a given sample
- print_samples_by_status_in_module - Prints the samples that PASS/WARN/FAIL a given module
- print_all_samples_orderby_status - Prints all samples ordered by PASS/WARN/FAILs
- print_all_modules_orderby_status - Prints all modules ordered by PASS/WARN/FAILs
- print_module_description - Prints textual description of given module
Press TAB (sometimes twice) to see every available command in the current context. TAB also autocompletes to supported commands.
- Print an overview of all the modules:
> print_module_stats
===========================================================================
=============================== MODULE STATS ==============================
===========================================================================
MODULE PASS WARN FAIL
Adapter Content 162 98 0
Basic Statistics 260 0 0
Kmer Content 0 0 260
Overrepresented sequences 0 259 1
Per base N content 260 0 0
Per base sequence content 0 1 259
Per base sequence quality 260 0 0
Per sequence GC content 8 96 156
Per sequence quality scores 260 0 0
Per tile sequence quality 238 22 0
Sequence Duplication Levels 0 31 229
Sequence Length Distribution 192 68 0
- List the sample that failed module Overrepresented sequences:
> print_samples_by_status_in_module
>> Module name: overrepresented_sequences
>>> Status: FAIL
SAMPLE NAME MODULE NAME STATUS FASTQ(s)
sample73 Overrepresented sequences FAIL 1
- Print details of sample73
> print_sample_details
>> Sample name: sample73
==========================================================================================
===================================== SAMPLE DETAILS =====================================
==========================================================================================
SAMPLE NAME PASS WARN FAIL
sample73 14 (58.33%) 1 (4.17%) 9 (37.50%)
================================= FASTQC DATA - FASTQ #1==================================
INFO VALUE
Sequences flagged as poor quality 0
Encoding Sanger / Illumina 1.9
Sequence length 101
File type Conventional base calls
Total Sequences 39996006
%GC 50
Filename 73_R1_001.fastq
================================= FASTQC DATA - FASTQ #2==================================
INFO VALUE
Sequences flagged as poor quality 0
Encoding Sanger / Illumina 1.9
Sequence length 101
File type Conventional base calls
Total Sequences 39996006
%GC 51
Filename 73_R2_001.fastq
======================================== MODULES =========================================
NAME FASTQ #1 FASTQ #2
Adapter Content PASS PASS
Basic Statistics PASS PASS
Kmer Content FAIL FAIL
Overrepresented sequences FAIL WARN
Per base N content PASS PASS
Per base sequence content FAIL FAIL
Per base sequence quality PASS PASS
Per sequence GC content FAIL FAIL
Per sequence quality scores PASS PASS
Per tile sequence quality PASS PASS
Sequence Duplication Levels FAIL FAIL
Sequence Length Distribution PASS PASS
- Open HTML report for FASTQ #1 in sample73 to check out the plots:
> open_sample_html_report
>> Sample name: sample73
>>> Read file number: 1
*opens report in webbrowser*
- NOTE: TAB auto-completion is your friend!
> print_module_d<TAB>
> print_module_description <ENTER>
>> Module name: ov<TAB>
>> Module name: overrepresented_sequences <ENTER>
...
It's written in Python 2.7. Python 2.6 seems to have issues with string formatting.
Experimental testing suggests Python 3 compatibility is easily achieved. Convert to Python 3 using 2to3:
2to3 -w *.py
Execute using Python 3:
python3 fastqc_browser.py -i fastqc_output_dir