• Compile and setup
• Usage & Output
• Performance
• Unit tests and code coverage
• Known issues

Fast and easy stats for FASTA and FASTQ files

Compile and setup

Assuming you are in the root directory of this project (i.e. where this README file is), compile the fxstat executable with:

gcc -O3 -Wall -g src/fxstat.c -lz -lm -o fxstat

Then move the fxstat executable to a directory of your choice like $HOME/bin/.

If you are on a Unix system, all the requirements should be satisfied as fxstat depends only on gcc for compilation and on standard C libraries.

Usage & Output

Usage should be straightforward. Assuming fxstat is on your PATH (if not, use path/to/fxstat):

fxstat -h
fxstat r1.fastq.gz r2.fastq.gz
fxstat sequence_dir/
cat reads.fastq | fxstat

Stat all *.fastq files in directory fastq_pass and in its subdirectories, pull all statistics in a single summary (default is one summary per file):

fxstat -p fastq_pass

For more control over files to include, consider using the find command. E.g.,

fxstat -p `find fastq_pass -name '*.fastq'

---

The output should be self explanatory:

[53oxa1_fast_nano.fastq.gz]
n_seq              35028
n_bases            365454001
mean_length        10433.20
median_length      8224.50
mean_read_quality  10.40
N0                 68226  # MAX length
N25                23612
N50                17594
N75                11909
N100               57  # MIN length > 0
A                  24.87%
T                  24.76%
C                  25.05%
G                  25.32%
N                  0.00%
GC                 50.37%
n_files: 1
# Proc time 00:00:07

The N50 is the sequence length of the shortest read at 50% of the total read length. Other Nx statistics are defined similarly for other thresholds.

Performance

Speed and ease of use should be the main features of fxstat. Quick & dirty benchmark on v0.1.0 commit 8c5290c. Test file is 370 Mbytes (compressed), 365 million bases:

time zcat 53oxa1_fast_nano.fastq.gz | wc > /dev/null

real    0m11.941s
user    0m20.965s
sys     0m0.395s

time fxstat 53oxa1_fast_nano.fastq.gz > /dev/null

real    0m7.572s
user    0m7.486s
sys     0m0.085s

Test file from:

curl -s https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRZ/011038/SRR11038963/53oxa1_fast_nano.fastq \
| gzip > 53oxa1_fast_nano.fastq.gz

Unit tests and code coverage

To run tests:

cd test
python test.py

Code coverage report will be in test/code_coverage.

Requirements for running the test suite:

• python should be available on virtually every system

• valgrind for checking memory leaks. If not available, install it with any package manager like apt or conda

• lcov for code coverage report. As above, install with a package manager or conda

Known issues

• There is no check the input files are correctly formatted