HISAT is a fast and sensitive spliced alignment program. As part of HISAT, it includes a new indexing scheme based on the Burrows-Wheeler transform (BWT) and the FM index, called hierarchical indexing, that employs two types of indexes: (1) one global FM index representing the whole genome, and (2) many separate local FM indexes for small regions collectively covering the genome. ned for mapping different types of RNA-seq reads. All these together, HISAT enables extremely fast and sensitive alignment of reads, in particular those spanning two exons or more. HISAT is distributed under theGPLv3 license.
Beside the index files under /fdb/hisat, HISAT on Biowulf has been built with sra support. A local copy of the SRA Refseq reference data is maintained in /fdb/sra/refseq, and the NCBI SRA toolkit has been configured on Biowulf to :
Version | Module Name | Alternate Module Name
Hisat2 v 2.2.1 | built for NCBI NGS v3.0.1 hisat/2.2.2.1-ngs3.0.1 | hisat2/2.2.1
| Hisat2 v 2.1.0 | built for NCBI NGS v2.10.9 hisat/2.2.1.0-ngs2.10.9 | hisat2/2.1.0
| |
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=10g salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load hisat [user@cn3144 ~]$ cd /data/$USER/hisat [user@cn3144 ~]$ hisat2 -p 4 -x $HISAT_INDEXES/grch38/genome -f $HISAT_HOME/example/reads/reads_1.fa \ -S /data/$USER/output.sam [user@cn3144 ~]$ hisat2 -p 4 -x $HISAT_INDEXES/grch38/genome -f $HISAT_HOME/example/reads/reads_1.fa \ $HISAT_HOME/example/reads/reads_2.fa -S /data/$USER/output.sam [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. hisat.sh). For example:
#!/bin/bash cd /data/$USER/mydir module load hisat hisat2 -p $SLURM_CPUS_PER_TASK -x $HISAT_INDEXES/grch38/genome -f $HISAT_HOME/example/reads/reads_1.fa \ -S /data/$USER/output1.sam hisat2 -p $SLURM_CPUS_PER_TASK -x $HISAT_INDEXES/grch38/genome -f $HISAT_HOME/example/reads/reads_1.fa \ $HISAT_HOME/example/reads/reads_2.fa -S /data/$USER/output2.sam ...... ......
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=4 --mem=10g hisat.sh
Create a swarmfile (e.g. hisat.swarm). For example:
cd dir1; hisat2 -p $SLURM_CPUS_PER_TASK -x $HISAT_INDEXES/grch38/genome \ -f $HISAT_HOME/example/reads/reads_1.fa -S /data/$USER/output1.sam cd dir2; hisat2 -p $SLURM_CPUS_PER_TASK -x $HISAT_INDEXES/grch38/genome \ -f $HISAT_HOME/example/reads/reads_1.fa -S /data/$USER/output1.sam cd dir3; hisat2 -p $SLURM_CPUS_PER_TASK -x $HISAT_INDEXES/grch38/genome \ -f $HISAT_HOME/example/reads/reads_1.fa -S /data/$USER/output1.sam [...]
Submit this job using the swarm command.
swarm -f hisat.swarm [-g 10] [-t 4] --module hisatwhere
-g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
-t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
--module hisat | Loads the hisat module for each subjob in the swarm |
This benchmarks used 3gb paired sequences. 16 cores is most efficient.
Core | Time(hr:min) |
---|---|
1 | 1:45:00 |
2 | 1:05:00 |
4 | 39:50 |
8 | 21:51 |
16 | 12:46 |
32 | 11:39 |