Assembltrie
Source Code

Assembltrie

Assembltrie is a software tool for compressing collections of (fixed length) Illumina reads, written in C++14 and is availble under an open-source license. Currently, Assembltrie is the only FASTQ compressor that approaches the information theory limit for a given short read collection uniformly sampled from an underlying reference genome. Assembltrie becomes the first FASTQ compressor that achieves both combinatorial optimality and information theoretic optimality under fair assumptions.

Installation

Assembltrie is suggested to compile with

  • GCC version 5.0 or higher (or equivalent GCC version that supports at least C++14)
  • Intel version 17.0 or higher

to generate reliable compression performance. Note that unlike most existing software tools, Assembltrie does not depend on any down-stream compressors, such as gzip or bzip2 so it is not necessary to install them. The tentative building process is as simple as

cd assembltrie
make

which will give an executable program astrie.

Usage

To run Assembltrie from command line, type

astrie -c -i <input.fastq> -o <result> [options]

for compression; and

astrie -d -i <input.out> -o <result> [options]

for decompression.

Compression. The mode -c implies to compress the input FASTQ file, generating two separate binary output (compressed) files: one named result.out, containing the encoding of assembled reads; the other named part.out, containing the encoding of singletons as well as other meta information necessary for decompression. In addition, options specifies the following mandatory and selectable parameters:

  • -L <integer> Mandatory, specifies the (fixed) read length in one compression run, the maximum value is L = 250
  • -K <integer> Mandatory, specifies the minimum overlap length/hash length, the suggested value is floor(L / 5) for L = 100
  • -h 0 | 1 | 2 Optional, h = 0 ignores any strand correction heuristic; h = 2 applies our greedy strand correction heuristic
  • -s <integer> Optional, accelerates potential children search by ignoring the already processed reads with suffix length less than or equal to integer, and the suggested value is floor(L / cov), where cov denotes the coverage of the input read collection (FASTQ file)
  • -e <integer> Optional, the maximum allowed mismatches for read overlaps. The default value is 3, but 4 is strongly recommended for L = 100 and 6 for L = 150
  • -n <integer> Optional, the number of working threads, defualt value is n = 8

Decompression. The mode -d implies to decompress the input compressed file input.out plus the available part.out into result.fasta, which contains a permutation (according to their locations in the constructed read forest) of (the sequence content only) of the original uncompressed read collection. To properly decompress input.out, Assembltrie expects the following parameters (the decompression process is restricted to a single thread)

  • -L <integer> Mandatory, the (fixed) read length in one compression run, should be the same as what is specified in the compression process.
  • -h 0 | 1 | 2 Mandatory, although in Assembltrie’s compression process it’s optional. Again, it should follow what is specified in the compression process.

Sample Usage

(export PATH=.:$PATH)
astrie -c -L100 -K20 -h0 -s4 -iSRR554369_1.fastq -oSRR554369_1.out -e4 -n8
astrie -d -L100 -h0 -iSRR554369_1.out -oSRR554369_1.fasta