SRST2 requires a specific naming convention for input fastq files

 SRST2 Trouble installing in server

 Also wanted to mention that SRST2 has been there for a while now (last updated was 2015) and I had some issues with running server because of dependency issues of bowtie2 tool (libstd, libtbb). 

 

SRST2 Trouble with specific versions of bowtie

 

Also, SRST2 only needs a specific version of bowtie2 (between 2.10 to 2.2.9 - but the latest is 2.4.1) causing some problem to work on server. 

 

SRST2 installation

 

Finally installed SRST2 on using conda. https://anaconda.org/bioconda/srst2

 

SRST2 requires a specific naming convention

 

An other issue with SRST2 is the naming, since it accepts the names like _S1_L001_R1_001.fastq.gz. 

For those samples which does not have a convention " _S1_L001_R1_001.fastq", created a symlink dummy with " _S1_L001_R1_001.fastq". 

For example, "filename_L001_R1_001.fastq" does not follow the SRST2 input convention, so created a symlink file filename_S1_L001_R1_001.fastq.