Main tool: IRMA
IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza, ebolavirus and coronavirus.
IRMA developers are aware of a problem with the Sars-Cov-2 module which will cause the software to crash because of an memory issue. This problem will be addressed in the upcoming release of 1.0.3 sometime in the near future. For the time being do not use IRMA for Sars-Cov-2.
#Paired-end files:
#USAGE: IRMA <MODULE-config> <R1.fastq.gz/R1.fastq> <R2.fastq.gz/R2.fastq> <sample_name>
#WARNING!!!! IRMA expects Illumunia Fastq formatting:
@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<xpos>:<y-pos> <read>:<is filtered>:<control number>:<index>
# If you are downloading samples from SRA please use the following code or IRMA's outputs will be empty
#SRR17940172 is used for an example; replace this with SRR id of fastq files that are needed
awk '{if(NR%2==1) $0=sprintf($1); print;}' SRR17940172_1.fastq > SRR17940172_1a.fastq && \
awk '{if(NR%4==1) $0=sprintf($1" 1:N:18:NULL"); print;}' SRR17940172_1a.fastq > SRR17940172_1.fastq && \
awk '{if(NR%2==1) $0=sprintf($1); print;}' SRR17940172_2.fastq > SRR17940172_2a.fastq && \
awk '{if(NR%4==1) $0=sprintf($1" 2:N:18:NULL"); print;}' SRR17940172_2a.fastq > SRR17940172_2.fastq
IRMA FLU Sample1_R1.fastq.gz Sample1_R2.fastq.gz Sample1
IRMA EBOLA Patient1_R1.fastq Patient1_R2.fastq MyPatient
IRMA FLU-utr Sample1_R1.fastq.gz Sample1_R2.fastq.gz Sample1WithUTRs
#Single read files:
#USAGE: IRMA <MODULE-config> <fastq/fastq.gz> <sample_name>
IRMA FLU SingleEndIllumina.fastq.gz MyIlluminaSample
IRMA FLU-pacbio ccs_reads.fastq MyPacBioSample
IRMA FLU-pgm pgm_reads.fastq MyIonTorrentSample
Better documentation can be found at https://wonder.cdc.gov/amd/flu/irma/
The manuscript can be found at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6