VATK

Virus Analysis Tool Kit

1. Evaluating your raw sequencing data

• counting sequences: fastq and fastq.gz
• quality assurance: FASTQC and samstats
• Determining the quality and complexity of next-generation sequencing data without a reference genome

2. trimming and de-multiplexing: Trimmomatic, Fastx_toolkit, fastx_trimmer, cutadapt, trim_galore, condetri, flexor (https://github.com/seqan/flexbar)
3. genotype detection, reference selection

• MIRNA_SEARCH

4. alignment: bowtie2, bwa, tanoti
5. post alignment stats:

• weeSAM - python script for various coverage statistics (legacy versions in perl)
• SamRemoveIndels - awk script to remove reads with indels from a SAM file
• UniqSamPE - awk script to remove paired-end fragments that start and end at the exact same position

6. post alignment analysis: haplotype window, remove primer reads, detecting chimeras
7. consensus calling
8. variant calling (link to ValVs)