TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by Ion Torrent sequencing technologies.
There are multiple versions of TMAP available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail TMAP
To select a module, type
module load TMAP/[ver]
where [ver] is the version of choice.
Environment variables set:
- $PATH
Sample session:
$ module load TMAP $ tmap mapall -n 8 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2> logfile.out
NOTE: By default, tmap will attempt to use ALL CPUS ON THE HOST. Please indicate the number of threads with the -n or --num-threads option.
Create a batch input file (e.g. tmap.sh), which uses the input file 'input.bam'. For example:
#!/bin/bash module load TMAP # Aligning to reference genome tmap mapall -n 8 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2>logfile.out
Submit this job using the Slurm sbatch command.
$ sbatch --cpus-per-task=8 --mem=20g tmap.sh
Create a swarmfile (e.g. tmap.swarm). For example:
tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output1.bam 2>logfile1.out tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output2.bam 2>logfile2.out tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output3.bam 2>logfile3.out tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output4.bam 2>logfile4.out
Submit this job using the swarm command.
$ swarm -f tmap.swarm -t 12 -g 20
Once an interactive job has been started,
sinteractive --cpus-per-task=8 --mem=20g
load the module and run the command.
module load TMAP tmap mapall -n 8 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2>logfile.out
- TMAP: The Novel, by Nils Homer
- Type tmap --help at the prompt.
