The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

• https://github.com/smithlabcode/preseq

• Module Name: preseq (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
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 preseq
[user@cn3144 ~]$ preseq lc_extrap -o yield_estimates.txt input.bed

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load preseq
preseq lc_extrap -o yield_estimates.txt input.bed

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

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

cd dir1; preseq lc_extrap -o yield_estimates.txt input.bed
cd dir2; preseq lc_extrap -o yield_estimates.txt input.bed
cd dir3; preseq lc_extrap -o yield_estimates.txt input.bed

Submit this job using the swarm command.

swarm -f job.swarm [-g #]--module preseq