SegPE Usage Documentation

0X01 installation environment

Installing Rust /Cargo

curl --proto '=https' --tlsv1.2 -sSf <https://sh.rustup.rs> | sh

Or upgrade, recommend upgrading to 1.77.0

rustup update stable

0X02 compile

Has been compiled for multi-platform/cross-platform use

Because of the use of SIMD acceleration, there will be differences on different CPUs :

Intel/ AMD x86 architecture CPU on

Modify Cargo.toml

[package.metadata.docs.rs]
features = ["simd_avx2"]

[target.'cfg(target_arch = "aarch64")'.dependencies]
block-aligner = { version = "0.5", features = ["simd_avx2"] }

Compile:

cargo build --features simd_avx2 --release

In theory, as long as the memory can withstand the memory required to read the FASTQ or the number of threads * batch_reads, there is no need to worry about memory overflow, so the number of threads can be used as much as possible.

0X03 CLI command parameter description

segpe --help
Algorithmic ideas of SegPE:
    - Exact match search: This is a more direct method for finding exact matches of artificial sequences.
    Regular expression matching and Hamming distance:
    This is suitable for detecting and locating index sequences, especially when mismatches of a certain length are taken into account.

    - Process and classify PE sequences: After removing the adapter and index sequences, classify the PE sequences and create new PE FASTQ files.

    - Use Multi-threads, SIMD and AsyncIO to handle large amounts of data.

Usage: segpe [OPTIONS] --five-art-fa <FIVE_ART_FA> --three-art-fa <THREE_ART_FA> --five-idx-fa <FIVE_IDX_FA> --pe1-fastq <PE1_FASTQ> --pe2-fastq <PE2_FASTQ>

Options:
      --five-art-fa <FIVE_ART_FA>
          Path of 5' artificial fasta file

      --three-art-fa <THREE_ART_FA>
          Path of 3' artificial fasta file

      --five-idx-fa <FIVE_IDX_FA>
          Path of 5‘ index fasta file

      --three-idx-fa <THREE_IDX_FA>
          Path of 3’ index fasta file

          [default: ]

      --idx-loc <IDX_LOC>
          Location of index, 1: PE1 2: PE2 3: both

          [default: 1]

      --pe1-fastq <PE1_FASTQ>
          Path of PE1 fastq file

      --pe2-fastq <PE2_FASTQ>
          Path of PE1 fastq file

  -s, --seed-len <SEED_LEN>
          Number of seed length, not allow to longer than index length

          [default: 6]

      --merge-pe
          Merged overlapped PE

      --error-tolerance <ERROR_TOLERANCE>
          Number of error tolerance

          [default: 1]

  -m, --match-score <MATCH_SCORE>
          Number of alignment macth score

          [default: 1]

      --error-score <ERROR_SCORE>
          Number of alignment mismacth score

          [default: -1]

      --gap-open-score <GAP_OPEN_SCORE>
          Number of alignment gap open score

          [default: -5]

      --gap-extend-score <GAP_EXTEND_SCORE>
          Number of alignment gap extend score

          [default: -1]

  -n, --num-threads <NUM_THREADS>
          Number of cucurrency threads

          [default: 8]

  -b, --batch <BATCH>
          batch size of reads, which every thread need to handle

          [default: 10000]

      --train <TRAIN>
          pretrain size of reads

          [default: 0]

      --trim-name
          add trim info in reads_name

  -o, --outdir <OUTDIR>
          Path of output directory

          [default: ./]

  -h, --help
          Print help (see a summary with '-h')

  -V, --version
          Print version

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