Hisat2 --sra-acc parameter not working


I have been for some time using hisat2 in the IFB Cluster with the parameter --sra-acc that allows mapping of reads directly from NCBI:SRA.
In the last weeks this parameter does not work anymore, with an error message: unrecognized option '--sra-acc'
Is there a possibility to make it work again?

From the hisat2 manual, apparently there is a need to install the NCBI-NGS toolkit:
"For the support of SRA data access in HISAT2, please download and install the NCBI-NGS toolkit. When running make, specify additional variables as follow. make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory, where NCBI_NGS_DIR and NCBI_VDB_DIR will be used in Makefile for -I and -L compilation options. For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used."

In my computer I did not have to do this, but it still works.

One remark. There are two versions of hisat2 in the cluster (2.1.0 and 2.2.1) and the option --sra-acc works in version 2.1.0 but not in version 2.2.1
Thanks in advance.

Hi Jose,

Unfortunately, it's not straight forward.
Maybe you can request a change for hisat2 (Issues · DaehwanKimLab/hisat2 · GitHub) or an integration with the conda package ? Or maybe download reads directly from NCBI:SRA ?

Hi dbenaben,

No problem. I am using version 2.1.0 and everything is working fine.
Thanks for your help.