SpeedSeq is a genome analysis platform designed for rapid whole-genome variant detection and interpretation

References:

• Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nature methods. 2015 Aug 10;12(10):966. doi: 10.1038/nmeth.3505

• SpeedSeq Main Site

• Module Name: speedseq (see the modules page for more information)
• Environment variables set
  • SPEEDSEQ_HOME
• Example files in $SPEEDSEQ_HOME/example

Allocate an interactive session and run the program.
Sample session (user input in bold) based on
$SPEEDSEQ_HOME/example/run_speedseq.sh:

[user@biowulf]$ sinteractive --cpus-per-task 2 --gres lscratch:10
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 speedseq
[+] Loading VEP 95 on cn3092 
[+] Loading singularity  on cn3092 
[+] Loading ROOT 6.13.02  ... 
[+] Loading gcc  7.3.0  ... 
[+] Loading cnvnator  0.3.3 
[+] Loading speedseq, version 0.1.2-20180208-4e60002... 
[user@cn3144 ~]$ speedseq align \
    -o example \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -p \
    -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    $SPEEDSEQ_HOME/example/data/NA12878.20slice.30X.fastq.gz
[user@cn3144 ~]$ speedseq var \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -t $SLURM_CPUS_PER_TASK \
    -o example \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    example.bam
[user@cn3144 ~]$ speedseq sv \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -o example \
    -B example.bam \
    -S example.splitters.bam \
    -D example.discordants.bam \
    -R $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta
[user@cn3144 ~]$ speedseq realign \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -o example.realign \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    example.bam
[user@cn3144 ~]$  
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. speedseq.sh). For example:

#!/bin/sh
set -e
module load speedseq

test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=2

speedseq align \
    -o example \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -p \
    -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    $SPEEDSEQ_HOME/example/data/NA12878.20slice.30X.fastq.gz

speedseq var \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -t $SLURM_CPUS_PER_TASK \
    -o example \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    example.bam

speedseq sv \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -o example \
    -B example.bam \
    -S example.splitters.bam \
    -D example.discordants.bam \
    -R $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta

speedseq realign \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -o example.realign \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    example.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] --gres lscratch:# speedseq.sh

Create a swarmfile (e.g. speedseq.swarm). For example:

speedseq align \
    -o example1 \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -p \
    -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    $SPEEDSEQ_HOME/example/data/NA12878.20slice.30X.fastq.gz
speedseq align \
    -o example2 \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -p \
    -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    $SPEEDSEQ_HOME/example/data/NA12878.20slice.30X.fastq.gz
speedseq align \
    -o example3 \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -p \
    -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    $SPEEDSEQ_HOME/example/data/NA12878.20slice.30X.fastq.gz
speedseq align \
    -o example4 \
    -M $(expr $SLURM_MEM_PER_NODE / 1000) \
    -t $SLURM_CPUS_PER_TASK \
    -T /lscratch/$SLURM_JOB_ID/speedseq \
    -p \
    -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \
    $SPEEDSEQ_HOME/example/data/human_g1k_v37_20_42220611-42542245.fasta \
    $SPEEDSEQ_HOME/example/data/NA12878.20slice.30X.fastq.gz

Submit this job using the swarm command.

swarm -f speedseq.swarm [-g #] -t # --gres lscratch:# --module speedseq