A host subtraction database for virus discovery in human cell line sequencing data
The SDB1 subtraction database designed for three human cell lines: Jurkat, HepG2, HuH7. Use GNU gunzip to extract the FASTA file.
Scripts for the analysis of data from an experiment on human cell lines infected with Sendai virus.
- fastq-filter-by-name.pl - Reads FASTQ and list of names. Writes smaller FASTQ missing named reads.
- SendaiExperiment/run_trimmomatic.sh - Trimmed the reads.
- SendaiExperiment/run_bowtie_align_to_sdb.sh - Mapped the reads to SDB.
- SendaiExperiment/subtract_mapped_reads.sh - Create FASTQ of the unmapped reads. Invokes fastq-filter-by-name.pl
- SendaiExperiment/generate_unmapped_reads.sh - Invoke subtract_mapped_reads on each set of reads.
A small demonstration of the subtraction pipeline.
- subtraction.HUH7.contigs.fasta - A sample database of host sequences.
- Demo_R1_reads.HuH7.SeV.RiboDepleted.fastq - A sample of R1 reads containing host + virus.
- Demo_R2_reads.HuH7.SeV.RiboDepleted.fastq - A sample of R2 reads containing host + virus.
- run_Demo_subtraction.sh - A script that extracts non-host heads.
The script requires a parameter: the path to the scripts directory. The script uses other scripts: run_trimmomatic.sh, fastq-filter-by-name.pl. The script assumes installed software: bowtie2-build, bowtie2, samtools, trimmomatic (and its adapter file). The script indexes the database, maps the reads, lists the mapped read names, creates fastq of unmapped reads.