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jsrc analyze

Common analysis tools for sequences: phylogenetic tree construction (with optional bootstrap support), motif discovery, QC summary, consensus calling, and variant comparison.

phylo

Pass in a FASTA, pick an algorithm, and get a Newick tree. Supports neighbor-joining (NJ) and UPGMA. The output works with any tree viewer. Good for a quick look at clustering relationships or as a starting point for more detailed phylogenetic analysis.

Bootstrap support is built in: pass -n/--bootstrap with the number of replicates (0 = off, default 0) and -seed for the random seed (default 42). When bootstrap ≥ 1, the tree is annotated with branch support values.

jsrc analyze phylo -fa sequences.fa -o tree.nwk -a nj
jsrc analyze phylo -fa seqs.fa -n 200 -seed 42 -o tree.nwk
  • -fa: input FASTA.
  • -o: output Newick tree file.
  • -a: algorithm, nj or upgma (default: nj).
  • -n/--bootstrap: number of bootstrap replicates (default 0; 0 = off).
  • -seed: random seed (default 42).

motif

Find conserved short motifs in promoters or sequence sets. Control the number of motifs and the width range. Useful for exploratory scans and iterative refinement.

jsrc analyze motif -fa promoters.fa -o motif_out -nmotifs 5 -minw 6 -maxw 12
  • -fa: input FASTA.
  • -o: output directory.
  • -nmotifs: number of motifs to detect (default: 5).
  • -minw: minimum motif width (default: 6).
  • -maxw: maximum motif width (default: 12).

qc

Assembly quality (FASTA), mapping statistics (SAM), variant overview (VCF), read depth (FASTQ) — all in one command. A quick way to tell whether your data is usable before moving to more complex analyses.

jsrc analyze qc -fa assembly.fa -sam aln.sam -vcf variants.vcf.gz \
  -fq r1.fq.gz r2.fq.gz -gs 520000000 --json
  • -fa: assembly FASTA for contig/N50/GC metrics.
  • -sam: SAM/SAM.GZ for mapping rate and depth statistics.
  • -vcf: VCF/VCF.GZ for SNP/INDEL summary.
  • -fq: FASTQ/FASTQ.GZ for read/base/depth stats.
  • -gs: genome size in bp, used with -fq for depth estimation.
  • --json: print JSON output.

msa_consensus

After multiple sequence alignment, this generates a consensus sequence and per-column conservation scores. It checks whether input sequence lengths differ significantly and pads shorter sequences with gaps if needed.

jsrc analyze msa_consensus -fa aligned.fa --json
  • -fa: input FASTA (usually aligned sequences).
  • --json: JSON output.

snpindel

Compare two sequences for differences without going through a full variant calling pipeline. Input a FASTA with two sequences, output SNP/INDEL statistics. Convenient for quick sample-to-sample comparisons.

jsrc analyze snpindel -fa pair.fa -id1 sampleA -id2 sampleB --json
  • -fa: FASTA containing at least two sequences.
  • -id1: sequence 1 ID (default: first sequence).
  • -id2: sequence 2 ID (default: second sequence).
  • --json: JSON output.