slag

slag performs seeded local assembly of genes and specific chromosomal regions from unassembled sequencing reads to reconstruct targeted genomic loci.

Key Features:

• Iterative local assembly: Retrieves matching reads with BLAST and assembles them iteratively using CAP3, PHRAP, SPAdes, Canu, or Unicycler for nucleotide or protein targets.
• Read fragmentation: Fragments reads to enable assembly of long-read data at lower coverage (e.g., 5×) using PHRAP or CAP3.
• Genome-complexity adaptability: Can assemble contigs that span entire chromosomes in simple, nonrepetitive genomes while contig growth is constrained in complex genomes by consensus contigs formed from repetitive sequences.
• Dependence on read characteristics: Contig length and accuracy scale with read length and accuracy, with pyrosequencing or Illumina reads producing contigs suitable for PCR primer design and Oxford Nanopore or pre-HiFi Pacific Biosciences long reads producing contigs primarily suitable for designing baiting sequences for further targeted sequencing.
• Low-coverage applicability: Effective for local assemblies from read sets with coverage below 20×, providing an alternative to ATRAM2.
• Empirical validation: Has been used to extend wheat gene sequences that were validated by cloning and Sanger sequencing of overlapping amplicons.

Scientific Applications:

• Targeted gene and locus reconstruction: Reconstruction of specific genes or chromosomal regions from unassembled reads for focused genomic analysis.
• Primer design: Generation of contigs from pyrosequencing or Illumina reads accurate enough for PCR primer design.
• Bait design for targeted sequencing: Production of contigs from Oxford Nanopore or pre-HiFi PacBio reads suitable for designing baits for further targeted sequencing.
• Low-coverage local assembly in complex genomes: Local assembly in species or datasets with limited coverage, exemplified by extensions of wheat gene sequences.

Methodology:

Iteratively retrieve target-matching reads using BLAST, optionally fragment reads, and assemble retrieved reads with CAP3, PHRAP, SPAdes, Canu, or Unicycler; support both nucleotide and protein target sequences.