Biodiversity and Evolution - Environmental Metagenomics & Metabarcoding

Koala (Phascolarctos cinereus) retrovirus (KoRV): identification of insertion sites and relationship to cancer- related genes

Authors: Fritz Lekschas, Annkatrin Bressin, Melanie Liedtke, Nina Kersten

Source code: https://github.com/flekschas/bio-div-korv

Transcript

2. ♥
5. ➢ ➢ ➢ ➢ ➢ ➢ h BASH
7. fqgrep –p PATTERN –m MISMATCHES \ –o OUTPUT.fastq INPUT.fastq[.gz]
8. java –jar trimmomatic.jar SE -phred33 \ -trimlog TRIM.log INPUT.fastq OUTPUT.fastq \ ILLUMINACLIP:/adapters/TruSeq3-SE.fa:2:30:10 \ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:14 \ MINLEN:30
9. bwa index -p PREFIX GENOME.fa bwa aln PREFIX READS.fastq > ALIGNMENT.bwa bwa samse PREFIX ALIGNMENT.bwa \ READS.fastq > ALIGNMENT.sam
11. dnaclust INPUT.fasta -l –s 0.8 \ -k 3 > OUTPUT.txt
12. seqlogo -F PNG -f INPUT.fasta -c > OUTPUT.png
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28. Analysis pipeline can be downloaded at: https://bitbucket.org/flekschas/biodivex1 Adjustable for other insertion site identification problems