# download and build longcallR
git clone https://github.com/huangnengCSU/longcallR.git
cd longcallR
cargo build --release
# call small variants from Nanopore cDNA reads
./longcallR -b input.bam -f ref.fa -o output -t 8 --platform ont --preset ont-cdna
# call small variants from Nanopore dRNA reads
./longcallR -b input.bam -f ref.fa -o output -t 8 --platform ont --preset ont-drna
# call small variants from PacBio iso-seq reads
./longcallR -b input.bam -f ref.fa -o output -t 8 --platform hifi --preset hifi-isoseq
# call small variants from PacBio mas-seq reads
./longcallR -b input.bam -f ref.fa -o output -t 8 --platform hifi --preset hifi-masseqLongcallR is a small variant caller for single molecule long-read RNA-seq data. LongcallR supports Nanopore cDNA sequecing and dRNA sequencing, PacBio Iso-Seq and MAS-Seq.
LongcallR is written in Rust and uses Cargo to build as follows:
git clone https://github.com/huangnengCSU/longcallR.git
cd longcallR
cargo build --release
General usage
./longcallR \
--bam-path input.bam \ ## The alignment bam file
--ref-path ref.fa \ ## The reference file must be indexed.
--platform ${PLATFORM} \ ## options: {ont, hifi}
--preset ${PRESET} \ ## option: {ont-cdna, ont-drna, hifi-isoseq, hifi-masseq}
--output ${OUTPUT_DIR}/${PREFIX} ## output path and prefix of output files
The following table shows the results of several datasets. WTC-11 Iso-Seq, WTC-11 ONT, HG002 MAS-Seq and HG004 MAS-Seq are public available. The ground truth of WTC-11 is described in Mark D. Robinson et.al paper. The ground truths of HG002 and HG004 are from GIAB NISTv4.2.1. All truth variants used for benchmarking have at least 10X coverage in the input. The results in sub-table (all sites) are obtained by hap.py. The sub-table (non-A-to-G sites) is achieved by removing all A-G and T-C substitutions from the results of hap.py. The sub-table (evaluation without genotype error) is for separating genotype errors from SNP discovery errors.
./longcallR -b demo/demo.bam -f demo/chr20.fa -o demo/test -t 8 --platform hifi --preset hifi-masseq
- Preset for Nanopore direct cDNA-Seq.
MIT License
Copyright (c) 2024 Dana-Farber Cancer Institute.
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