RAILS and Cobbler

RAILS and Cobbler perform scaffolding and automated gap filling of draft genome assemblies to improve contiguity and completeness using long DNA sequences such as scaftigs, contigs or long reads from Pacific Biosciences and Oxford Nanopore.

Key Features:

• Scaffolding (RAILS): Orders and orients contig sequences based on alignment information using a scaffolding engine developed for SSAKE and LINKS.
• Gap patching (Cobbler): Aligns long DNA sequences to draft assemblies, tallies alignments, and replaces ambiguous 'N' regions with corresponding sequences from the inputs.
• Combined scaffolding and filling: RAILS both scaffolds draft assemblies and fills the newly created or existing gaps with provided long DNA sequences.
• Long-sequence input: Leverages long, preferably high-quality sequences such as scaftigs, contigs, or long reads derived from other genome drafts or platforms including Pacific Biosciences and Oxford Nanopore.
• Alignment-based replacement: Uses alignment tallies to select and insert sequences that replace Ns in the assembly draft.
• Implementation: Both programs are implemented in PERL.

Scientific Applications:

• Draft genome finishing: Automated finishing of draft de novo genome assemblies by closing gaps represented by 'N's and improving sequence continuity.
• Scaffolding with long reads or scaftigs: Ordering and orienting contigs using long sequences from other drafts or long-read platforms to increase assembly contiguity.
• Performance on human-derived data: In simulations using long sequences from the human genome reference, Cobbler closed over 65% of gaps with a correlation of closed gaps to length estimates of R=0.8253.
• Contiguity improvement: Using the same data, RAILS increased assembly N50 from 5.6 Mbp to 7.3 Mbp (approximately 30% improvement).

Methodology:

Align long DNA sequences to the draft assembly, tally alignments, replace 'N' regions with aligned sequences, and perform ordering/orienting of contigs using a scaffolding engine developed for SSAKE and LINKS; both programs are implemented in PERL.