README.md

IRMA-RSV

Run IRMA RSV module

For pair read: IRMA <RSV0-config> <R1.fastq.gz/R1.fastq> <R2.fastq.gz/R2.fastq> <sample_name> For single read: IRMA <RSV0-config> <fastq/fastq.gz> <sample_name>

Run IRMA RSV with pseudo-segment (to fix the low QC, usually the homopolymer issue)

IRMA <RSV1-config> <fastq/fastq.gz> <sample_name_RSV1>
IRMA <RSV2-config> <fastq/fastq.gz> <sample_name_RSV2>

Nesting RSV pseudo-segment Library output

Assembly RSV sequence read with pseudo-segments instead of WGS can fix some low QC reads Two RSV module: RSV-SHGF library and RSV-without SHGF library are created due the interest of RSV cell surface genomes.

To run the nesting scripts

RSV IRMA output directoryies, .sh, reference directory, java screipts need to be moved under a same directory IRMA output from different libraries need to be labeled as _"RSV1" and _"RSV2"

On Local

Gene alignment tool MAFFT need to be installed under ./src

## Compile the java
javac ./nest.java
sh comb.sh >> comb.log

On Server

## Add module load MAFFT in shell script

javac ./nest.java
sh comb.sh >> gacrc_comb.log

How this pipeline works

Step1: .sh will check the exists of IRMA output _RSV1 and _RSV2 directories and amended_consensus sub directories.

Step2: The ORF of different gene regions are searched by allignment with reference sequence considering the possible issue at the intergenic regions.

Step3: Different gene regions from IRMA consensus read are nested together.

Step4: Alignment with reference sequence file is also generated.

Step5: sum.txt be created contain the genotype and length information for all RSV samples under the directory; Recommend to generate comb.log to double check if all samples have been processed correctly.