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Program settings and metrics

Reference notes for how each Lucimics tool runs, what inputs it expects, and what outputs it generates.

Genome Scan

Genome Scan summarizes assembly inputs with QC signals such as GC% and N50/L50. Use it to validate basic assembly health before diving into read-level alignment.

  • Inputs: FASTA reference assembly.
  • Prechecks: contig count, total length, GC%, min/max contig size.
  • Metrics: GC%, N50/L50, total length, contig distribution.

Read Viewer

Read Viewer visualizes BAM alignments against a FASTA reference. Use window size controls to zoom and inspect coverage patterns or base-level alignment detail.

  • Inputs: FASTA reference + one or more BAM files.
  • Window size: controls coverage granularity and base-level view threshold.
  • Outputs: coverage histogram, read alignments, per-window summaries.

Minimap2

Minimap2 runs sequence alignment workflows in-browser and produces alignment outputs for downstream inspection.

  • Inputs: query reads + reference FASTA, plus presets tuned for short or long reads.
  • Behavior: aligns sequences using the selected preset and reports mapping stats.
  • Outputs: alignment files and summary metrics for downstream review.

Samtools

Samtools manipulates and inspects sequence alignment files. Use it to convert SAM to BAM, sort and index alignments, and summarize mapping statistics.

  • Inputs: a SAM or BAM alignment file.
  • Subcommands: view (SAM↔BAM conversion), sort (coordinate-sort BAM), index (build BAI for a sorted BAM), flagstat (alignment summary).
  • Outputs: converted/sorted alignment files, index files, or text statistics depending on the subcommand.

Seqtk

Seqtk is a fast utility for processing FASTA and FASTQ sequence files. Use it to convert formats, extract subsequences, and apply lightweight filters before alignment.

  • Inputs: a FASTA or FASTQ file (plus a region or name list for subseq).
  • Subcommands: seq (format conversion and filtering), subseq (extract regions or named records).
  • Outputs: a transformed FASTA or FASTQ file.

Read Check

Read Check validates FASTA and FASTQ files before they enter a pipeline. Use it to catch malformed input early — encoding errors, mixed alphabets, or corrupted records.

  • Inputs: a FASTA or FASTQ file.
  • Behavior: runs sequential checks for binary content, file size, encoding, and nucleotide vs. protein alphabet; surfaces warnings and blocking errors.
  • Outputs: a validation report — no transformed file is produced.