https://ics.hutton.ac.uk/tablet/ Download & Install 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). # Install Tablet-viewer on Ubuntu/Linux (Version 1.16.09.06 - Sep 2016) wget http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_1_17_08_17.shchmod a+x tablet_linux_x64_1_16_09_06.shsudo ./tablet_linux_x64_1_16_09_06.sh# start tablet by typing in the command line: tabletVisualize .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 .bamsamtools sort SAMPLE.bam -o SAMPLE_sorted.bam # sort .bam filesamtools 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  |