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combinator-FQ

Combinator-FQ is a tool for detecting adjacent contigs and calculating the LQ-coefficient. The LQ-coefficient reflects the degree of connection between contigs. The higher the LQ-coefficient, the higher is the degree of connection.

Latest version: 1.6.a.

Description

Combinator-FQ identifies adjacent contigs in order to facilitate further scaffolding.

Format of input: multi-fasta file containing contigs.

Combinator-FQ supports contigs assembled by SPAdes and A5.

It calculates LQ-coefficient, defined as follows:

Length of overlap is further referred to as k. k-start (k-end) denotes contig's prefix (suffix) of length k.

Ends of contigs are considered adjacent in following situations:

combinator-FQ calculates expected length of the genome as follows:

If no coverage information is present in sequence headers, multiplicity is calculated based on discovered overlaps of the i-th contig as follows:

Dependencies

Combinator-FQ is written in Python, so you need Python interpreter (version 3.X) to use it. Here you can download Python.

Explanation of output files

Combinator-FQ generates 3 output files:

1) Table containing information about contigs adjacency:

<prefix>_combinator_adjacent_contigs.tsv

Format of table is following:

#  Contig name  Length  Coverage  GC(%)  Multiplicity  Annotation  Start         End
1  NODE_1...    304356  93.7155   34.12  1.2           [empty]     [S=E(NODE_22); ovl=127]  [E=rc_E(NODE_26); ovl=99]
...

Explanation of "Start" and "End" columns:

  • [S=E(NODE_22); ovl=127] means that k-start (S) of contig NODE_1... is identical to k-end (E) of contig NODE_22, and overlap length is 127 (ovl=127).

  • [E=rc_E(NODE_26); ovl=99] means that k-end of contig NODE_1... is identical to reverse complement (rc_) k-end of contig NODE_26, and overlap length is 99 (ovl=99).

2) File, in which all matchings (not only adjacency-associated) are listed:

<prefix>_combinator_full_matching_log.txt

3) Brief summary:

<prefix>_combinator_summary.txt

Options

-h (--help): print help message;

-v (--version): print version;

-i (--mink): minimum k (in b.p.) to consider.
  Value: integer > 0; Default if 21 b.p.

-a (--maxk): maximum k (in b.p.) to consider.
  Value: integer > 0; Default is 127 b.p.

-k (--k-mer-len): exact k (in b.p.).
  If specified, '-i' and '-a' options are ignored.
  Value: integer > 0; Option is disabled by default;

-o (--outdir): output directory;
  Default value: 'combinator-result'

Examples

  ./combinator-FQ.py contigs.fasta -k 127 -o my_outdir

  ./combinator-FQ.py another_contigs.fa -i 25 -a 300 -o my_outdir

If input file is omitted in the command (like in the command below), combinator-FQ will process all fasta files in the working directory.

  ./combinator-FQ.py -i 25 -a 300 -o my_outdir