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legoseq

Manipulating sequencing data is like playing with LEGO bricks.

Features

  • The DNA sequence is segmented into blocks based on the Fix (Anchor) sequence, with the flexibility of freely combining these blocks using jinja2 templates.

  • Supports for the demultiplex of sequence based on the index(barcode).

  • Compatible with a variety of sequencing platforms, including Illumina, Pacbio, and Nanopore.

  • Accepts inputs in fasta/fastq formats.

  • Supports single end and pair end inputs; for paired-end sequencing, currently, only read1 is available for free combination.

  • Facilitates parallel computing, ensuring rapid processing speeds.

Install

Source

If the Rust compiler and associated Cargo are installed, legoseq may be installed via

git clone git@github.com:dongspy/legoseq.git
cd legoseq
cargo build --release
target/release/legoseq --help

Quick Start

blockinfo

The software supports block types of Fix, Variable, Index.

  • Fix refers to a given sequence of bases, which needs to be provided in advance, and legoseq uses an alignment algorithm to determine the position of the Fix sequence in the read;

  • Variable refers to the variable sequence, which needs to be determined according to the upstream and downstream Fix sequences;

  • Index refers to the barcode sequence of a sample, which can be used for demultiplexing;

For details, see test/data/blockinfo.tsv

template

Generate the corresponding sequence file according to the jinja2 template.

>{{read.name}} {{Fix_2.seq[:6]}} len={{read.seq|length}}
ATCG{{read.seq}}AAA{{Variable_3.seq}}

test

cd test

sh  run_pair_end.sh #  pair-end fastq as input

sh run_pair_end_fa.sh # pair-end fasta as input

sh run_single_end.sh # single-end fastq as input