【2.7.1】ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates

1. trimming of primers and low-quality bases,
2. consensus calling,
3. variant calling - both iSNVs and insertions/deletions,
4. identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.

一、安装

cd /data4/covid19/
git clone https://github.com/andersen-lab/ivar.git
cd ivar
./autogen.sh
./configure
make
make install

三、报错

sam@c01 ivar]$ ivar --help
ivar: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

[root@c01 samtools-1.9]# find /data/software/  -name libhts.so.3
/data/software/anaconda3/pkgs/htslib-1.10.2-h78d89cc_0/lib/libhts.so.3
/data/software/anaconda3/pkgs/htslib-1.17-h6bc39ce_1/lib/libhts.so.3
/data/software/anaconda3/pkgs/htslib-1.16-h6bc39ce_0/lib/libhts.so.3
/data/software/ngsAnalysis/smrtlink_v11/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/htslib/htslib_1.13/lib/libhts.so.3
/data/software/ngsAnalysis/delly/src/htslib/libhts.so.3
/data/software/nanopolish.bak/htslib/libhts.so.3
/data/software/nanopolish/htslib/libhts.so.3


cp /data/software/nanopolish/htslib/libhts.so.3 /usr/local/lib

四、我的案例

ivar trim -b /opt/ref/ARTICv3.bed -p ${output}/${ID}/${ID}.trimmed.bam -i ${output}/${ID}/${ID}.bam -q 15 -m 50 -s 4

参考资料

• https://github.com/andersen-lab/ivar