% CLONOTYPER(1) clonotypeR User Manual

NAME

clonotyper - Quantitative analysis of antigen receptor sequences

SYNOPSIS

clonotypeR detect library1.fastq library2.fastq ...

clonotypeR extract library1 library2 ...

DESCRIPTION

clonotypeR detect

Detects the V segments using the bwa bwasw. This command uses by default as many threads as possible (see THREADS).

clonotypeR extract

Extracts the CDR3s and records the clonotypes in one file per library. This command is not running threaded programs, so there may be a benefit running multiple extractions in parallel.

OPTIONS

ClonotypeR's options are passed as environment variables.

CLONOTYPER_REFERENCE

Path to reference alignments. If not set, a references directory is searched in /etc, /usr/share/clontyper, and then in the parent directory.

CLONOTYPER_SCRIPTS

Path to clonotypeR's accessory scripts. If not set, a scripts directory is searched in /usr/share/clontyper, and then in the parent directory.

CLONOTYPES

Path to the directory where the clonotypes are to be extracted.

Default: ./clonotypes

DEBUG

Save intermediate files (vectorstrip output) for troubleshooting.

Default: unset

EXTRACT_DIR

Path to the BAM and temporary files. Default: ./extraction_files

TMPDIR

Use the directory indicated by TMPDIR to store temporary files.

THREADS

Number of threads for the alignment

VS_MISMATCH

Percentage of mismatches tolerated when detecting the boundaries of the CDR3 region. The alignment is made with 20 base pairs.

Default: 0

FILES

LICENSE

Public domain: http://creativecommons.org/publicdomain/zero/1.0/