NAME

       MakeDb.py - Repertoire clonal assignment toolkit (Python 3)

DESCRIPTION

       usage: MakeDb.py [--version] [-h]  ...

       Create tab-delimited database file to store sequence alignment information

   help:
       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

   subcommands:
              Aligner used

       igblast
              Process igblastn output.

              igblast-aa

              Process igblastp output.

       imgt   Process IMGT/HighV-Quest output (does not work with V-QUEST).

       ihmm   Process iHMMune-Align output.

   output files:
              db-pass

              database  of  alignment  records  with  functionality  information,  V and J calls, and a junction
              region.

              db-fail

              database with records that fail due to no productivity information, no gene  V  assignment,  no  J
              assignment, or no junction region.

   universal output fields:
              sequence_id,  sequence,  sequence_alignment, germline_alignment, rev_comp, productive, stop_codon,
              vj_in_frame,   locus,   v_call,   d_call,   j_call,   junction,   junction_length,    junction_aa,
              v_sequence_start,     v_sequence_end,    v_germline_start,    v_germline_end,    d_sequence_start,
              d_sequence_end,    d_germline_start,     d_germline_end,     j_sequence_start,     j_sequence_end,
              j_germline_start, j_germline_end, np1_length, np2_length, fwr1, fwr2, fwr3, fwr4, cdr1, cdr2, cdr3

   imgt specific output fields:
              n1_length,   n2_length,   p3v_length,   p5d_length,   p3d_length,  p5j_length,  d_frame,  v_score,
              v_identity, d_score, d_identity, j_score, j_identity

   igblast specific output fields:
              v_score,  v_identity,  v_support,  v_cigar,  d_score,  d_identity,  d_support,  d_cigar,  j_score,
              j_identity, j_support, j_cigar

   ihmm specific output fields:
              vdj_score

   10X specific output fields:
              cell_id,  c_call,  consensus_count,  umi_count,  v_call_10x, d_call_10x, j_call_10x, junction_10x,
              junction_10x_aa

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

MakeDb.py 1.0.1                                   October 2020                                      MAKEDB.PY(1)