Chromosomer

Chromosomer is a reference-assisted assembly tool for producing draft chromosome sequences. It provides the following routines:

• fragmentmap - produce a fragment map from fragment alignments to reference chromosomes;
• assemble - obtain FASTA sequences of assembled chromosomes from a fragment map;
• transfer - move annotated regions from original fragments to assembled chromosomes;
• fragmentmapstat - get summary on a fragment map;
• fragmentmapbed - convert a fragment map to the BED format (e.g., for viewing in a genome browser);
• fastalength - get lengths of sequences in a FASTA file (required for fragmentmap).

Installation

We recommend to install Chromosomer by using pip:

pip install chromosomer

pip will automatically resolve Chromosomer dependencies and install missing packages.

Assembling chromosomes

A typical chromosome assembly involves two steps. First, a fragment map is derived from fragment alignments to reference chromosome sequences. Second, FASTA sequences of the assembled chromosomes are obtained from the produced fragment map and the original fragment sequences.

The first step is carried out with fragmentmap in the following way:

chromosomer fragmentmap alignment_file gap_size fragment_lengths output_map

The second step is implemented in the assemble routine:

chromosomer assemble map fragment_fasta output_fasta