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Tablet

Tablet - short read alignment viewer

https://ics.hutton.ac.uk/tablet/

Using Tablet for visual exploration of second-generation sequencing data
Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, Shaw PD and Marshall D
Briefings in Bioinformatics 14(2), 193-202 (2013).

Download & Install

# download latest version from:
https://ics.hutton.ac.uk/tablet/download-tablet/

# install Tablet-viewer on Ubuntu/Linux (replace xx with downloaded version)
chmod a+x tablet_linux_x64_x_xx_xx_xx.sh
sudo ./tablet_linux_x64_x_xx_xx_xx.sh

# start tablet by typing in the command line:
tablet

Visualize .bam file of short read alignments

# 1) map short reads against a reference sequence
→ bowtie2

# 2) create sorted and indexed bam file
samtools view -b -S SAMPLE.sam > SAMPLE.bam   # convert .sam to .bam
samtools sort SAMPLE.bam -o SAMPLE_sorted.bam # sort .bam file
samtools index SAMPLE_sorted.bam              # create index (.bam.bai file)

# 3) open in tablet sorted bam file (and related reference sequence)
[Open Assembly]
SAMPLE_sorted.bam
REF.fasta