Ngs-bits
Introduction
Ngs-bits
- Short-read sequencing tools.
Versions
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 -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
ml biocontainers ngs-bits
SeqPurge -in1 input1_1.fastq input2_1.fastq \
-in2 input2_2.fastq input2_2.fastq \
-out1 R1.fastq.gz -out2 R2.fastq.gz