Tablet

Tablet - short read alignment viewer

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

http://tablet.hutton.ac.uk/en/latest/data_visualization.html

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

sudo source tablet_linux_x64_1_21_02_08.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