Biobambam

Introduction

Biobambam is a collection of tools for early stage alignment file processing.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/biobambam
Home page: https://gitlab.com/german.tischler/biobambam2

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.0.183

BELL

2.0.183

GAUTSCHI

2.0.183

NEGISHI

2.0.183

SCHOLAR

2.0.183

Commands

  • bam12auxmerge

  • bam12split

  • bam12strip

  • bamadapterclip

  • bamadapterfind

  • bamalignfrac

  • bamauxmerge

  • bamauxmerge2

  • bamauxsort

  • bamcat

  • bamchecksort

  • bamclipXT

  • bamclipreinsert

  • bamcollate2

  • bamdepth

  • bamdepthintersect

  • bamdifference

  • bamdownsamplerandom

  • bamexplode

  • bamexploderef

  • bamfastcat

  • bamfastexploderef

  • bamfastnumextract

  • bamfastsplit

  • bamfeaturecount

  • bamfillquery

  • bamfilteraux

  • bamfiltereofblocks

  • bamfilterflags

  • bamfilterheader

  • bamfilterheader2

  • bamfilterk

  • bamfilterlength

  • bamfiltermc

  • bamfilternames

  • bamfilterrefid

  • bamfilterrg

  • bamfixmateinformation

  • bamfixpairinfo

  • bamflagsplit

  • bamindex

  • bamintervalcomment

  • bamintervalcommenthist

  • bammapdist

  • bammarkduplicates

  • bammarkduplicates2

  • bammarkduplicatesopt

  • bammaskflags

  • bammdnm

  • bammerge

  • bamnumericalindex

  • bamnumericalindexstats

  • bamrank

  • bamranksort

  • bamrecalculatecigar

  • bamrecompress

  • bamrefextract

  • bamrefinterval

  • bamreheader

  • bamreplacechecksums

  • bamreset

  • bamscrapcount

  • bamseqchksum

  • bamsormadup

  • bamsort

  • bamsplit

  • bamsplitdiv

  • bamstreamingmarkduplicates

  • bamtofastq

  • bamvalidate

  • bamzztoname

Module

You can load the modules by:

module load biocontainers
module load biobambam

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run biobambam on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=biobambam
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers biobambam

# Your biobambam workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=biobambam
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers biobambam

# Your biobambam workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=biobambam
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers biobambam

# Your biobambam workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=biobambam
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers biobambam

# Your biobambam workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=biobambam
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers biobambam

# Your biobambam workflow...