Introduction

Sfasta is a replacement for the FASTA/Q format with the twin goals of saving space and having very fast random-access, even for large datasets (such as the nt database, 203Gb gzip compressed, 210Gb bgzip compressed(+1.8Gb index), and 141Gb with sfasta, index inclusive).

Speed comes from assuming modern hardware, thus:

• Multiple compression threads by default
• Dedicated I/O Threads
• Modern compression algorithms (ZSTD, as default)
• Fractal Index
• Everything stored as sequence streams (like stored with like, for better compression)

The goals are random-access speed by query or random, and smaller size. It supports other compression algorithms, which could be used for archival purposes (such as xz compression).

Community Feedback Period

I'm hopeful folks will check this out, play around, break it, and give feedback.

Usage

Installation

cargo install sfasta Don't have cargo?

Usage

Compression

To compress a file:

sfa convert MyFile.fasta

#You can also convert directly from gzipped files:
sfa convert MyFile.fasta.gz

Compression profiles are supported. The built-in ones can be accessed with --fast, --fastest, --small, --smallest.

sfa convert --fast reads.fastq
sfa convert --fastest reads.fastq

Fast / Fastest are optimized for fast reading and random access, while Small / Smallest are optimized for size of file on disk. These are in development, let me know what works best for you

You can specify your own profile, using a template from GitHub as an starting point:

sfa convert -p myprofile.yml reads.fastq

You can use other compression schemes. The software automatically detects which is used and decompresses accordingly.

sfa convert --snappy MyFile.fasta
sfa convert --xz MyFile.fasta

# Reading the file "just works"
sfa view MyFile.sfasta 

You can also change the block size. Smaller blocks will speed up random access, while larger blocks will increase compression ratios. 512 (512kb, 524288 bytes) is default.

# This will create 8Mb blocks
sfa convert --block-size 8192 MyFile.fasta

View a file:

sfa view MyFile.sfasta

Query a file by sequence ID:

sfa faidx MyFile.sfasta Chr1

For help:

sfa --help

Requirements

Should work anywhere that supports Rust. Tested on Ubuntu, Red Hat, and Windows 10. I suspect it will work on Mac OS. WASM support is forthcoming.

Details

Compression Types Supported

Type	Status	Notes
ZSTD	Default	Optimized
Brotli	Implemented	Could be more optimized
LZ4	Implemented	Rust implementation does not support levels
XZ	Implemented	Slow, high compression
Snappy	Implemented	Not recommended
GZIP	Implemented	Not recommended
BZIP2	Implemented	Not recommended
NONE		No compression, supported

Compression can be set per data type

• You can use ZSTD for sequence compression, XZ for masking, Brotli for IDs and Headers, for example.
• Compression profiles are found in compression_profiles folder and are stored as YAML.
• You can load your own compression profile from the command line.
• IDs are interpreted from FASTA/Q files as the part before the space on an identified line, for example

  >Chr1 This is the chromosome
  ^---^ ^--------------------^
  ID    Header

  The same rule applies for FASTQ.

Data Types Supported

Data	Status
Sequences	Fully supported, nucleotide, amino, and RNA (anything, really)
Sequence IDs	Fully Supported
Additional Header Information	Fully Supported
Quality Scores	Fully Supported
Masking	Fully Supported
Flags	Planned
Nanopore Signals	Planned
Base Modifications	Planned
Pangenome Graph	Maybe
Alignments	Not Planned. CRAM fulfills this role.
Variants	Too different, another solution needed.

Comparisons

Features

Compression Type	Random Access	Multithreaded	Tools
sfasta	Yes	Yes	sfa
gzip	No	Yes	gzip, pigz, crabz
bgzip	Yes	Yes	bgzip, crabz
NAF	No	No	naf
ZSTD	No	Yes	zstd

Benchmarks

Uniprot Random Access

Using UniProt SWISS-Prot release 2024_02. File size is ~88Mb.

Samtools index pre-built with samtools faidx uniprot_sprot.fasta.gz with a bgzip compressed file.

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
sfa faidx uniprot_sprot.sfasta "sp\|Q8CIX8\|LGSN_MOUSE" "sp\|O31861\|YOJB_BACSU" "sp\|B2XTX0\|PSAJ_HETA4" "sp\|A2YNP0\|SPX6_ORYSI" "sp\|P69474\|CAPSD_CGMVS"	16.5 ± 0.3	15.7	18.2	1.00
samtools faidx uniprot_sprot.fasta.gz "sp\|Q8CIX8\|LGSN_MOUSE" "sp\|O31861\|YOJB_BACSU" "sp\|B2XTX0\|PSAJ_HETA4" "sp\|A2YNP0\|SPX6_ORYSI" "sp\|P69474\|CAPSD_CGMVS"	456.9 ± 6.8	451.8	474.9	27.75 ± 0.66

Uniprot Size

Uncompressed: 272M

Compression Type	Size
sfasta (index incl)	71Mb
NAF (no index)	66Mb
zstd (no index)	76Mb
bgzip (excl. index)	88Mb
bgzip (incl. index)	111Mb (88Mb + 23Mb)
pigz (no index)	89Mb

• SFASTA contains an index, where the other formats do not. An fai index is 23Mb for this uniprot.
• SFASTA uses a higher compression level for zstd as default, as well as stream compression like NAF, thus the smaller size.

❯ ls -lah uniprot_sprot.fasta.gz.fai
-rw-rw-r-- 1 joseph joseph 23M Apr 26 17:02 uniprot_sprot.fasta.gz.fai

UniProt Size (sfa profiles)

Profile	Size
smallest	59Mb
small	62Mb
default	68Mb
fast	73Mb
fastest	78Mb

Uniprot Compression Speed

Command	Mean [s]	Min [s]	Max [s]	Relative
sfa convert --threads 14 uniprot_sprot.fasta	1.543 ± 0.057	1.458	1.648	3.67 ± 0.34
bgzip -kf --threads 16 uniprot_sprot.fasta	1.293 ± 0.042	1.187	1.345	3.08 ± 0.28
pigz -kf -p 16 uniprot_sprot.fasta	0.959 ± 0.017	0.934	0.990	2.28 ± 0.20
ennaf --protein --temp-dir /tmp uniprot_sprot.fasta -o uniprot_sprot.naf	1.078 ± 0.008	1.069	1.094	2.57 ± 0.22
zstd -k uniprot_sprot.fasta -f -T16	0.420 ± 0.035	0.363	0.485	1.00
crabz -f bgzf -p 16 uniprot_sprot.fasta -o uniprot_sprot.fasta.gz	0.674 ± 0.017	0.649	0.703	1.60 ± 0.14

Compression speed is slower, but this is primarily due to the index creation. For bgzip samtools takes 2.07 seconds to generate the index. Also of note is pigz, ennaf, and zstd do not support indexing, while crabz does (using bgzf format).

Nanopore Reads

As a FASTA file.

Nanopore Reads Compression Speed

Command	Mean [s]	Min [s]	Max [s]	Relative
sfa convert nanopore.fasta	22.844 ± 2.973	18.514	26.591	3.37 ± 0.45
ennaf nanopore.fasta --temp-dir /tmp	19.231 ± 0.158	19.003	19.505	2.84 ± 0.10
bgzip -k --index -f --threads 7 nanopore.fasta	82.065 ± 0.478	81.559	82.720	12.10 ± 0.42
pigz -k -p 7 nanopore.fasta -f	83.118 ± 0.994	82.055	85.015	12.26 ± 0.44
crabz -p 7 nanopore.fasta > nanopore.fasta.crabz	82.933 ± 1.268	81.313	84.412	12.23 ± 0.46
zstd -k nanopore.fasta -f -T7	6.780 ± 0.232	6.484	7.220	1.00

Nanopore Reads Random Access

Samtools index pre-built

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
sfa faidx nanopore.sfasta ae278260-d941-45c9-9e76-40f04ef8e56c	83.6 ± 10.6	71.7	98.5	1.00
samtools faidx nanopore.fasta.gz ae278260-d941-45c9-9e76-40f04ef8e56c	752.6 ± 5.8	746.7	764.8	9.01 ± 1.15

Nanopore Reads Size

Uncompressed Size: 8.8G	Compression Type	Size
NAF (no index)	2.2G
sfasta (incl index)	2.6G
bgzip (excl index)	2.6G
zstd (no index)	2.7G

Genome

Genome Random Access Speed

Samtools index pre-built

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
sfa faidx Erow_1.0.sfasta PXIH01S0167520.1	135.3 ± 9.4	129.4	153.4	1.09 ± 0.09
samtools faidx Erow_1.0.fasta.gz PXIH01S0167520.1	189.7 ± 10.2	182.2	215.7	1.53 ± 0.10

Genome Compression Speed

Command	Mean [s]	Min [s]	Max [s]	Relative
sfa convert Erow_1.0.fasta	4.847 ± 0.189	4.579	5.199	2.39 ± 0.16
ennaf Erow_1.0.fasta --temp-dir /tmp	8.054 ± 0.044	7.986	8.155	3.97 ± 0.22
bgzip -k --index -f --threads 10 Erow_1.0.fasta	7.522 ± 0.510	6.639	8.132	3.71 ± 0.32
pigz -k -p 10 Erow_1.0.fasta -f	7.593 ± 0.110	7.353	7.965	3.75 ± 0.21
crabz -p 10 Erow_1.0.fasta > Erow_1.0.crabz	7.530 ± 0.203	7.317	7.992	3.72 ± 0.23
zstd -k Erow_1.0.fasta -f -T10	2.026 ± 0.112	1.834	2.273	1.00

Genome Size

Uncompressed: 2.7G

Compression Type	Size
NAF (no index)	446M
sfasta (incl index)	596M
bgzip (excl index)	635M
Zstd (no index)	663M

Illumina Reads

11Gb of reads (FASTQ)

Compression Speed

Command	Mean [s]	Min [s]	Max [s]	Relative
sfa convert --threads 14 reads.fastq	80.794 ± 3.379	77.700	87.570	9.59 ± 0.53
bgzip -kf --threads 16 reads.fastq	48.920 ± 0.264	48.645	49.279	5.81 ± 0.21
pigz -kf -p 16 reads.fastq	80.712 ± 1.461	78.945	83.181	9.58 ± 0.39
ennaf --dna --fastq --temp-dir /tmp reads.fastq -o reads.naf	38.276 ± 0.246	37.951
38.602	4.54 ± 0.17
zstd -k reads.fastq -f -T16	8.423 ± 0.303	7.915	8.889	1.00
crabz -f bgzf -p 16 reads.fastq -o reads.fastq.gz	22.176 ± 3.802	17.889	26.813	2.63 ± 0.46

File size

Uncompressed: 2.7G

Compression Type	Size
NAF (no index)	1.9Gb
sfasta (incl index)	2.5Gb
bgzip (excl index)	2.4Gb (+ 2.8Gb index )
Zstd (no index)	2.5Gb

Future Plans

Implement NAF-like algorithm

NAF has an advantage with 4bit encoding. It's possible to implement this, and use 2bit when possible, to gain additional speed-ups. Further, there is some SIMD support for 2bit and 4bit DNA/RNA encoding.

Subsequence support for faidx CLI

Only open the block(s) that contain the subsequence. The index is already set up to support this and I've had it working before in the python bindings.

Additional Speed-ups

There is plenty of room for speed improvements, including adding more threads for specific tasks, CPU affinities, native compilation, and maybe more Cow.

C and Python bindings

To make it easier to use in other programs and in python/jupyter

Small file optimization

Sfasta is currently optimized for larger files.

GFA file format support

Graph genome file format is in dire need of an optimized format

Profile Guided Optimization

Never mind. This somehow doubled the time it takes to compress binaries. Enable PGO for additional speed-ups

Fuzzing

The following format parsers are fuzzed. To fuzz execute the following in the libsfasta directory:

cargo fuzz run parse_fastq  -- -max_len=8388608
cargo fuzz run parse_fasta  -- -max_len=8388608
cargo fuzz run parse_sfasta -- -detect_leaks=0 -rss_limit_mb=4096mb -max_len=8388608

FAQ

I get a strange symbol near the progress bar

You need to install a font that supports Unicode. I'll see if there is a way to auto-detect.

Why so many dependencies?

Right it it works with a wide range of compression functions. Once some are determined to be the best others could be dropped from future versions. The file format itself has a version identifier so we could request people rollback to an older version if they need to.

Why samtools comparison?

I've got plenty of experiments trying to get a fast gzip compressed multi-threaded reader, but even when mounted on a ramdisk, it is too slow. Samtools is an awesome, handy tool that has the 'faidx' function, which I use almost constantly. While faidx is a handy utility function, it is not optimized for large datasets, thus the test is a little unfair. Still, it's helpful to have something to compare to.

File Format

The format is found in the docs.