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