Software: Ngs-bits
Description
Ngs-bits - Short-read sequencing tools.
Available Versions
| Unspecified: | 2022_04 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/ngs-bits and its home page on Github.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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