Guided reassembly

Use scarab reassemble after recruitment when you want a new assembly guided by an xPG or another trusted genome FASTA. Both commands use the same installed SCARAB environment, including SPAdes; no separate environment or Snakemake configuration is required.

Start with one target

scarab reassemble \
  -i SCARAB_out/algo_defaults/Default/xpgs/target.xPG.fasta \
  -l read_list.txt \
  -o reassembly \
  --threads 8 --memory 32

Replace the example FASTA with an actual xPG from your recruitment output. AutoOpt method and setting directories depend on your run; consult the log and output guide. To process several targets, pass their FASTA directory to -i. Discovery is nonrecursive and accepts .fa, .fna, and .fasta; use uncompressed input FASTAs and unique basenames. References, read files and adapters must remain outside the output directory.

The read list is headerless: one interleaved short-read FASTQ or two tab-separated R1/R2 paths per row. Relative paths resolve from the working directory, as in recruit. Paired FASTQs may be gzip-compressed. This command is for paired short reads; the recruitment command’s HiFi mode is not a reassembly mode. Use a separate output for reassembly, preserving recruitment results.

What runs

For each target and library, minimap2 uses its short-read preset. Primary alignments are retained only when both mates are mapped. Secondary and supplementary alignments are excluded. SAMtools groups names and extracts paired reads; libraries are processed separately so repeated read names do not become cross-library pairs. Unpaired alignments are not assembly input.

BBTools repairs pairing and BBDuk removes adapters and trims low-quality sequence. Settings follow the existing guided-reassembly recipe: right-end k-mer trimming (k=23, mink=11, hdist=1, paired overlap handling), quality trimming at 10, and minimum read length 75. Paired identifiers and counts are checked before assembly. SPAdes runs with --isolate and the target FASTA as --trusted-contigs. Trusted sequence can bias reconstruction; inspect read support and genome quality rather than treating the result as a validated complete genome.

Resources and outputs

Option

Meaning

--threads, -t

Threads for the active target; default 1. Targets run sequentially.

--memory

SPAdes memory limit in GB; default 16. BBTools heap is capped at the smaller of this value and 4 GB. This is not an operating-system memory limit for the whole command.

--adapters

Optional adapter FASTA. Normally discovered beside the installed BBTools executable.

--keep-intermediates

Preserve successful mapping, QC and SPAdes work directories.

--force

Preserve previous output in a sibling backup and start a fresh run.

The output contains reassembly_summary.tsv, run provenance/status JSON and one directory per target. Successful targets have contigs.fasta, scaffolds.fasta, reassembly.json, commands.log and spades.log. The summary reports mapped and clean pair counts and final sequence paths. Targets with no usable pairs are explicitly recorded as skipped_no_usable_pairs; they do not produce invented assembly files.

Intermediate work is removed after a successful or explicitly skipped target unless requested otherwise. Failure preserves diagnostic files and exits nonzero. A matching completed run can be invoked again to reuse its results. An interrupted or changed run requires a fresh output or --force; this first implementation does not resume individual failed SPAdes stages.

Container users must bind all input paths and a writable output directory. See installation and resources.