ChromoSort reference-guided assembly curation

chromo cut

Use chromo cut when you already know the exact breakpoint position for one or more contigs and want a transparent FASTA edit without running the alignment planner in chromo fix.

Positions are 1-based and mean “cut after this base.” For example, cutting a 10 bp contig at position 4 emits bases 1-4 and 5-10. Terminal cuts are rejected because they would create empty pieces.

Run chromo cut

Repeat --cut for multiple contigs, and use commas for multiple positions on the same contig:

chromo cut \
  --assembly-fasta assembly.fa \
  --cut contig_1:234567,450000 \
  --cut contig_2:10000 \
  --output-fasta results/sample.cut.fa \
  --report results/sample.cut_contigs.tsv

For a single contig, the original explicit form is also supported:

chromo cut \
  --assembly-fasta assembly.fa \
  --contig contig_1 \
  --pos 234567 450000 \
  --output-fasta results/sample.cut.fa \
  --report results/sample.cut_contigs.tsv

For batch review, provide a simple cuts file:

contig	position
contig_1	234567	450000
contig_2	10000

Then run:

chromo cut \
  --assembly-fasta assembly.fa \
  --cuts-file reviewed_cuts.tsv \
  --output-fasta results/sample.cut.fa \
  --report results/sample.cut_contigs.tsv

chromo cut Outputs

Output Description
--output-fasta Full assembly FASTA with requested contigs replaced by cut pieces. Uncut contigs are copied unchanged.
--report TSV report describing every emitted cut piece, including original contig, new contig, slice coordinates, piece length, and cut positions.

Cut pieces are named CONTIG_cut001, CONTIG_cut002, and so on by default. Change the inserted text with --name-separator, or use --simple-headers to write only the new FASTA IDs in cut-piece headers.

Example chromo cut Output

Table 1. Example cut report rows. Cutting contigA after bases 20 and 50 emits three adjacent slices and records the complete cut set on each row.

original_contig new_contig part_index slice_start slice_end piece_bp cut_after_positions
contigA contigA_cut001 1 1 20 20 20,50
contigA contigA_cut002 2 21 50 30 20,50
contigA contigA_cut003 3 51 80 30 20,50

Listing 1. Example cut FASTA records. Requested contigs are replaced by cut pieces; unrequested contigs are copied through unchanged.

>contigA_cut001
AAAAAAAAAAAAAAAAAAAA
>contigA_cut002
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>contigA_cut003
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>contigB
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

chromo cut Parameters

Parameter Default Meaning
--assembly-fasta required Assembly FASTA containing the contigs to cut.
--assembly-fai auto Optional FASTA index used for length validation. Defaults to <assembly-fasta>.fai when present.
--cut none Reviewed cut as CONTIG:POS[,POS...]; may be repeated.
--cuts-file none Optional file with contig and one or more cut positions per line.
--contig / --pos none Convenience form for one contig with one or more positions.
--output-fasta required New FASTA path. The input FASTA is never modified.
--report required TSV report path for the cut pieces.
--min-piece-bp 1 Reject cut plans that create pieces shorter than this length.
--name-separator _cut Text inserted before the numeric suffix.
--simple-headers off Write cut-piece FASTA headers containing only the new sequence ID.