diff --git a/README.md b/README.md index 3ca2c39..2a37578 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,34 @@ LiftOn is a homology-based lift-over tool using both DNA-DNA alignments (from Liftoff, credits to Dr. Alaina Shumate) and protein-DNA alignments (from miniprot, credits to Dr. Heng Li) to accurately map annotations between genome assemblies of the same or different species. LiftOn employs a two-step protein maximization algorithm to improve the annotation of protein-coding genes in the T2T-CHM13 JHU RefSeqv110 + Liftoff v5.1 annotation. The latest T2T-CHM13 annotation generated by LiftOn is available as JHU_LiftOn_v1.0_chm13v2.0.gff3 (ftp://ftp.ccb.jhu.edu/pub/data/LiftOn/JHU_LiftOn_v1.0_chm13v2.0.gff3) .
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Installation#

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Install through pip#

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LiftOn is on PyPi now. Check out all the releases here. Pip automatically resolves and installs any dependencies required by LiftOn.

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$ pip install LiftOn
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Install from source#

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You can also install LiftOn from source. Check out the latest version +!

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$ git clone https://github.com/Kuanhao-Chao/LiftOn
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+$ python setup.py install
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Why LiftOnâť“#

  1. Burgeoning number of genome assemblies: As of December 2023, there are 30,530 eukaryotic genomes, 567,228 prokaryotic genomes, and 66,429 viruses listed on NCBI (NCBI genome browser). However, genome annotation is lagging behind. As more high-quality assemblies are generated, we need an accurate lift-over tool to annotate them.