Ngs-bits

Introduction

Ngs-bits - Short-read sequencing tools.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/ngs-bits
Home page: https://github.com/imgag/ngs-bits

Note

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

Versions

Cluster

Version(s)

ANVIL

2022_04

BELL

2022_04

GAUTSCHI

2022_04

NEGISHI

2022_04

SCHOLAR

2022_04

Commands

  • SampleAncestry

  • SampleDiff

  • SampleGender

  • SampleOverview

  • SampleSimilarity

  • SeqPurge

  • CnvHunter

  • RohHunter

  • UpdHunter

  • CfDnaQC

  • MappingQC

  • NGSDImportQC

  • ReadQC

  • SomaticQC

  • VariantQC

  • TrioMaternalContamination

  • BamCleanHaloplex

  • BamClipOverlap

  • BamDownsample

  • BamFilter

  • BamToFastq

  • BedAdd

  • BedAnnotateFreq

  • BedAnnotateFromBed

  • BedAnnotateGC

  • BedAnnotateGenes

  • BedChunk

  • BedCoverage

  • BedExtend

  • BedGeneOverlap

  • BedHighCoverage

  • BedInfo

  • BedIntersect

  • BedLiftOver

  • BedLowCoverage

  • BedMerge

  • BedReadCount

  • BedShrink

  • BedSort

  • BedSubtract

  • BedToFasta

  • BedpeAnnotateBreakpointDensity

  • BedpeAnnotateCnvOverlap

  • BedpeAnnotateCounts

  • BedpeAnnotateFromBed

  • BedpeFilter

  • BedpeGeneAnnotation

  • BedpeSort

  • BedpeToBed

  • FastqAddBarcode

  • FastqConcat

  • FastqConvert

  • FastqDownsample

  • FastqExtract

  • FastqExtractBarcode

  • FastqExtractUMI

  • FastqFormat

  • FastqList

  • FastqMidParser

  • FastqToFasta

  • FastqTrim

  • VcfAnnotateFromBed

  • VcfAnnotateFromBigWig

  • VcfAnnotateFromVcf

  • VcfBreakMulti

  • VcfCalculatePRS

  • VcfCheck

  • VcfExtractSamples

  • VcfFilter

  • VcfLeftNormalize

  • VcfSort

  • VcfStreamSort

  • VcfToBedpe

  • VcfToTsv

  • SvFilterAnnotations

  • NGSDExportGenes

  • GenePrioritization

  • GenesToApproved

  • GenesToBed

  • GraphStringDb

  • PhenotypeSubtree

  • PhenotypesToGenes

  • PERsim

  • FastaInfo

Module

You can load the modules by:

module load biocontainers
module load ngs-bits

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 ngs-bits 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=ngs-bits
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ngs-bits

# Your ngs-bits 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=ngs-bits
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ngs-bits

# Your ngs-bits 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=ngs-bits
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ngs-bits

# Your ngs-bits 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=ngs-bits
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ngs-bits

# Your ngs-bits workflow...

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

module --force purge
module biocontainers ngs-bits

# Your ngs-bits workflow...