TQSLE

TQSLE v1.0 released

author: Huiguang Yi ([email protected])

Current version is based on x86_64 linux system

Dependencies:

1. gcc && gfortran (make sure gfortran is installed)
2. intel mkl BLAS (Recommended) or OpenBLAS or native BLAS (not Recommended)
3. SuiteSparse (need CHOLMOD module)

Install:

If intel mkl is available

make MKL_LIB=dir_path_contain_your_mkl_lib MKL_IOMP5=dir_path_contain_your_mkl_iomp5

Else If OpenBLAS/other BLAS is available

make BLAS_LIB=dir_path_contain_your_openblas

Else Use OpenBLAS in the repo

make

Usage:

# index construction
tqsle index -f<mean fragment size> -i <reference.fa> -o <outpath>

# quantification 
tqsle quant -i <indexpath> -o <outputpath> <reads.fastq>

Cite:

Huiguang Yi and others, A fast and globally optimal solution for RNA-seq quantification, Briefings in Bioinformatics, 2023;, bbad298, https://doi.org/10.1093/bib/bbad298