Reference Sequence and Capture Intervals Preparation for ExoClasma Suite
Project description
exoclasma-index
Description
exoclasma-index is a tools for reference sequence and capture intervals preparation, a part of upcoming ExoClasma Suite.
Features:
- Prepare FASTA reference sequence (purge names, uncompress, sort and filter contigs, etc.)
- Create restriction sites for Juicer as described at
config.json
. For now available restrictases include:- HindIII
- DpnII
- MboI
- Sau3AI
- Arima
- Add your own restriction sites.
- Create indices for:
- SAMtools (
samtools faidx
) - BWA (
bwa index
) - optional: GATK (
gatk CreateSequenceDictionary
)
- SAMtools (
Also, the tool can check and prepare exome BED files (captures).
This is a pre-release. Use it at your own risk!
Installation
python3 -m pip install exoclasma-index
Command-line dependencies
First three are available at Ubuntu repos:
apt install samtools bwa bedtools
GATK should be installed into Miniconda environment as described by the developer.
Usage
Reference preparation
exoclasma-index Reference -f ${FastaFile} -n ${ReferenceName} -p ${ParentDirectory}
Optional: -d ${ReferenceDescription}
, --no-gatk
, -c ${Contigs}
.
Contigs may be filtered or sorted with -c
option.
Full list of FASTA contigs can be displayed via
exoclasma-index Contigs -f ${FastaFile}
Capture preparation
exoclasma-index Capture -b ${BedFile} -n ${CaptureName} -g ${GenomeInfoJSON}
GenomeInfoJSON
is a JSON file which created via exoclasma-index Reference
.
Optional: -d ${ReferenceDescription}
Restriction sites manipulation
Restriction sites can be displayed, added, or removed:
exoclasma-index RestrictionSites
exoclasma-index AddRS -n ${RestrictionSiteName} -r ''${RestrictionSiteRegExp}''
exoclasma-index RemoveRS -n ${RestrictionSiteName}
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