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A emoji based bioinformatics command line tool

Project description


FASTQ with Emoji = FASTQE ๐Ÿค”

Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason.

Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and print a corresponding emoji!



Latest release versions of fastqe are available via pip or BioConda:

pip install fastqe

conda install -c bioconda fastqe


Development version can be isntall from this repository in the master branch.


fastqe can display usage information on the command line via the -h or --help argument:

usage: fastqe [-h] [--minlen N] [--scale] [--version] [--mean]
              [--custom CUSTOM_DICT] [--bin] [--noemoji] [--min] [--max]
              [--output OUTPUT_FILE] [--long READ_LENGTH] [--log LOG_FILE]
              [FASTQ_FILE [FASTQ_FILE ...]]

Read one or more FASTQ files, compute quality stats for each file, print as
emoji... for some reason.๐Ÿ˜„

positional arguments:
  FASTQ_FILE            Input FASTQ files

optional arguments:
  -h, --help            show this help message and exit
  --minlen N            Minimum length sequence to include in stats (default
  --scale               show relevant scale in output
  --version             show program's version number and exit
  --mean                show mean quality per position (DEFAULT)
  --custom CUSTOM_DICT  use a mapping of custom emoji to quality in
                        CUSTOM_DICT (๐Ÿ๐ŸŒด)
  --bin                 use binned scores (๐Ÿšซ๐Ÿ’€๐Ÿ’ฉโš ๏ธ๐Ÿ˜„๐Ÿ˜†๐Ÿ˜Ž๐Ÿ˜)
  --noemoji             use mapping without emoji (โ–โ–‚โ–ƒโ–„โ–…โ–†โ–‡โ–ˆ)
  --min                 show minimum quality per position
  --max                 show maximum quality per position
  --output OUTPUT_FILE  write output to OUTPUT_FILE instead of stdout
  --long READ_LENGTH    enable long reads up to READ_LENGTH bp long
  --log LOG_FILE        record program progress in LOG_FILE


fastqe will summarise FASTQ files to display the max, mean and minumum quality using emoji. To convert a file into this format, rather than summarise, you can use the companion program biomojify that will convert both sequence and quality information to emoji:

$ cat test.fq
@ Sequence
$ biomojify fastq test.fq
โ–ถ๏ธ  Sequence

Intall with pip install biomojify, and see the biomojify page for more information:


fastqe test.fastq

fastqe --min test.fastq

fastqe --max test.fastq

fastqe --max -min -bin test.fastq

Teaching Materials

Command line and NGS Introduction

This lesson introduces NGS process in the command line using by using the results of FASTQE before and after quality filerting using fastp:

Rachael St. Jacques, Max Maza, Sabrina Robertson, Guoqing Lu, Andrew Lonsdale, Ray A Enke (2019).
A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!.
NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis, (Version 2.0).
QUBES Educational Resources. doi:10.25334/Q4D172


A Galaxy wrapper is available from the IUC toolshed. Contact your Galaxy Admin if you would like to have it installed. A Galaxy Tutorial using FASTQE is in development.

FASTQE in Galaxy


FASTQE started out as part of PyCon Au presentations:

Responsive image


  • version 0.0.1 at PyCon Au 2016:
    • Mean position per read
  • version 0.0.2 at PyconAu 2017:
    • update emoji map
    • Max and minimum scores per position added
    • Wrapper code based on early version of Bionitio added
    • prepare for PyPi
  • version 0.1.0 July 2018
    • clean up code
    • add binning
  • version 0.2.6 July 2020
    • refactor code
    • add long read support with --long
    • add --noemoji for block-based output on systems that don't support emoji
    • add --custom for user-defined mapping to emoji
    • add --output to redirect to file instead of stdout
    • add gzip support
    • add redirect from stdin support
    • fix bug of dropping position if some sequences are only 0 quality
  • Galaxy Wrapper created July 2020
  • biomojify created July 2020


  • Reads up to 500bp only Read length above 500bp allowed but must be set by user with --long MAX_LENGTH
  • Same emoji for all scores above 41


This program is released as open source software under the terms of BSD License


  • pyemojify
  • BioPython
  • NumPy


  • Rearrange emoji to use more realistic ranges (i.e > 60 use uncommon emoji) and remove inconsistencies
  • Add conversion to emoji sequence format, with/without binning, for compressed fastq data fits into
  • Rewrite conversion to standalone function for use in iPython etc.
  • Teaching resources
  • Test data and unit tests
  • Add FASTA mode for nucleotide and proteins emoji see
  • MultiQC plugin
  • Galaxy Wrapper: available form the IUC toolshed

Rather convert to emoji than summarise? We've just started biomojify for that:


  • Andrew Lonsdale
  • Bjรถrn Grรผning
  • Catherine Bromhead
  • Clare Sloggett
  • Clarissa Womack
  • Helena Rasche
  • Maria Doyle
  • Michael Franklin
  • Nicola Soranzo
  • Phil Ewels


Use the --scale option to include in output.

0 ! ๐Ÿšซ
1 " โŒ
2 # ๐Ÿ‘บ
3 $ ๐Ÿ’”
4 % ๐Ÿ™…
5 & ๐Ÿ‘พ
6 ' ๐Ÿ‘ฟ
7 ( ๐Ÿ’€
8 ) ๐Ÿ‘ป
9 * ๐Ÿ™ˆ
10 + ๐Ÿ™‰
11 , ๐Ÿ™Š
12 - ๐Ÿต
13 . ๐Ÿ˜ฟ
14 / ๐Ÿ˜พ
15 0 ๐Ÿ™€
16 1 ๐Ÿ’ฃ
17 2 ๐Ÿ”ฅ
18 3 ๐Ÿ˜ก
19 4 ๐Ÿ’ฉ
20 5 โš ๏ธ
21 6 ๐Ÿ˜€
22 7 ๐Ÿ˜…
23 8 ๐Ÿ˜
24 9 ๐Ÿ˜Š
25 : ๐Ÿ˜™
26 ; ๐Ÿ˜—
27 < ๐Ÿ˜š
28 = ๐Ÿ˜ƒ
29 > ๐Ÿ˜˜
30 ? ๐Ÿ˜†
31 @ ๐Ÿ˜„
32 A ๐Ÿ˜‹
33 B ๐Ÿ˜„
34 C ๐Ÿ˜
35 D ๐Ÿ˜›
36 E ๐Ÿ˜œ
37 F ๐Ÿ˜‰
38 G ๐Ÿ˜
39 H ๐Ÿ˜„
40 I ๐Ÿ˜Ž
41 J ๐Ÿ˜

Binned scale:

0 ! ๐Ÿšซ
1 " ๐Ÿšซ
2 # ๐Ÿ’€
3 $ ๐Ÿ’€
4 % ๐Ÿ’€
5 & ๐Ÿ’€
6 ' ๐Ÿ’€
7 ( ๐Ÿ’€
8 ) ๐Ÿ’€
9 * ๐Ÿ’€
10 + ๐Ÿ’ฉ
11 , ๐Ÿ’ฉ
12 - ๐Ÿ’ฉ
13 . ๐Ÿ’ฉ
14 / ๐Ÿ’ฉ
15 0 ๐Ÿ’ฉ
16 1 ๐Ÿ’ฉ
17 2 ๐Ÿ’ฉ
18 3 ๐Ÿ’ฉ
19 4 ๐Ÿ’ฉ
20 5 โš ๏ธ
21 6 โš ๏ธ
22 7 โš ๏ธ
23 8 โš ๏ธ
24 9 โš ๏ธ
25 : ๐Ÿ˜„
26 ; ๐Ÿ˜„
27 < ๐Ÿ˜„
28 = ๐Ÿ˜„
29 > ๐Ÿ˜„
30 ? ๐Ÿ˜†
31 @ ๐Ÿ˜†
32 A ๐Ÿ˜†
33 B ๐Ÿ˜†
34 C ๐Ÿ˜†
35 D ๐Ÿ˜Ž
36 E ๐Ÿ˜Ž
37 F ๐Ÿ˜Ž
38 G ๐Ÿ˜Ž
39 H ๐Ÿ˜Ž
40 I ๐Ÿ˜
41 J ๐Ÿ˜


Use a dictionary of Pyemojify mappings in a text file instead of built in emoji choices:

'#': ':no_entry_sign:',
'\"': ':x:',
'!': ':japanese_goblin:',
'$': ':broken_heart:'

Emoji characters can also be used directlty instead (experimental):

'#': ':no_entry_sign:',
'\"': ':x:',
'!': '๐Ÿ‘ฟ',
'$': ':broken_heart:'

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