Usage:   panaln [combine /index /align] <options>  
--------------  
Function: combine  generate pangenome file  
          index    construct a pangenome index  
          align    perform read alignment  
--------------  
Feedback Email: <guolilu@stu.xidian.edu.cn> 

Usage: panaln combine -s <input.fasta> -v <input.vcf> -b <basename>  
--------------  
Specific:  -s STRING [required] reference genome  
           -v STRING [required] vcf file  
           -b STRING [required] basename  
           -c STRING [optional] context size (default:150)  
Please use ABSOLUTE PATHs when specifying files.  
--------------  
Feedback Email: <guolilu@stu.xidian.edu.cn>  

Usage: panaln index -p <input.pan>  
--------------  
Specific:  -p STRING [required] pangenome file  
Please use ABSOLUTE PATHs when specifying files.  
--------------  
Feedback Email: <guolilu@stu.xidian.edu.cn>  

Usage: panaln align -x <index_basename> -f <input.fastq> -s <output.sam>  
--------------  
Specific:  -x STRING [required] basename  
           -f STRING [required] fastq file  
           -s STRING [required] smm file  
Please use ABSOLUTE PATHs when specifying files.  
--------------
Feedback Email: <guolilu@stu.xidian.edu.cn>

git clone https://github.com/Lilu-guo/panaln.git
cd panaln/FM/  
make
cd ../semiWFA/
make
cd ../
make

./panaln combine -s /home/dell198/gll/panaln/Test/1.fa -v /home/dell198/gll/panaln/Test/1.fa.vcf -b chr1

./panaln index -p /home/dell198/gll/panaln/dirPan/chr1.pan

./panaln align -x /home/dell198/gll/panaln/dirPan/chr1 -f /home/dell198/gll/panaln/Test/1.fastq -s /home/dell198/gll/panaln/Test/1.sam

Illumina reads dataset:   
 https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_indexes/AshkenazimTrio/sequence.index.AJtrio_Illumina_2x250bps_06012016_updated.HG004   
PacBio-CCS reads dataset:   
 https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_10kb/m54238_180628_014238.Q20.fastq   
Common small variants:   
 http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp144Common.txt.gz   
Synthetic reads simulator:   
 https://github.com/DaehwanKimLab/hisat2/blob/master/hisat2_simulate_reads.py    
Pipeline of variant calling:   
 https://github.com/ksahlin/strobealign/blob/main/evaluation.md