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)

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

• SAMtools
• BWA
• BEDtools
• GATK

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}