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