Assemble Ecotype specific Lake Trout genomes

[sr320]

Using PacBio data assemble draft genome for two ecotypes..

https://github.com/RobertsLab/project-lake-trout

[kubu4]

FYI - These are both running on Klone, using Flye.

I previously used this on the C.bairdii long reads.

[sr320]

can you also do assemblies with hifiasm?

[kubu4]

Both are now also running on Klone, using hifiasm.

[kubu4]

Currently waiting on Flye assembly of Siscowet to finish.

Here are finished assemblies:

Flye

Lean:

• FastA (3.9GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-genome-assembly-lean/snam-lean-pb-flye-assembly.fasta

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-genome-assembly-lean/snam-lean-pb-flye-assembly.fasta.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-genome-assembly-lean/snam-lean-pb-flye-assembly.fasta.fai

hifiasm

Lean:

Primary assembly:

• FastA (3.5GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-assembly.fa

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-assembly.fa.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-assembly.fa.fai

Haplotype 1:

• FastA (3.2GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-hap1-assembly.fa

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-hap1-assembly.fa.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-hap1-assembly.fa.fai

Haplotype 2:

• FastA (2.7GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-hap2-assembly.fa

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-hap2-assembly.fa.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-hap2-assembly.fa.fai

Siscowet

Primary assembly:

• FastA (3.8GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-assembly.fa

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-assembly.fa.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-assembly.fa.fai

Haplotype 1:

• FastA (3.4GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-hap1-assembly.fa

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-hap1-assembly.fa.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-hap1-assembly.fa.fai

Haplotype 2:

• FastA (3.2GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-hap2-assembly.fa

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-hap2-assembly.fa.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-hap2-assembly.fa.fai

[kubu4]

I'll compare assemblies and get stats (N50, longest contigs, etc) using QUAST and post here.

[kubu4]

Okay, Flye Siscowet is finished:

Flye

Lean:

• FastA (4.1GB): https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-genome-assembly-siscowet/snam-siscowet-pb-flye-assembly.fasta

• MD5: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-genome-assembly-siscowet/snam-siscowet-pb-flye-assembly.fasta.md5

• FastA index: https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.1-genome-assembly-siscowet/snam-siscowet-pb-flye-assembly.fasta.fai

[kubu4]

Notebook post comparing assemblies, using QUAST:

https://robertslab.github.io/sams-notebook/posts/2026/2026-04-10-Genome-Comparisons---Lake-Trout-PacBio-Assemblies-Flye-vs-hifiasm-Using-QUAST/

HTML Report:

https://gannet.fish.washington.edu/gitrepos/project-lake-trout/output/13.2-genome-assembly-comparisons/report.html

Here's overview table, in Markdown:

Assembly	lean_flye	lean_hifiasm	siscowet_flye	siscowet_hifiasm
# contigs (>= 0 bp)	112562	33035	110158	24184
# contigs (>= 1000 bp)	112160	33035	109812	24184
# contigs (>= 5000 bp)	106095	33002	104705	24177
# contigs (>= 10000 bp)	81886	31353	84765	23609
# contigs (>= 25000 bp)	37973	21447	41932	17566
# contigs (>= 50000 bp)	17083	13735	18607	12107
Total length (>= 0 bp)	4046369763	3733314870	4336778941	4008351139
Total length (>= 1000 bp)	4046083421	3733314870	4336539268	4008351139
Total length (>= 5000 bp)	4023676535	3733170075	4318011635	4008320038
Total length (>= 10000 bp)	3840245419	3719588210	4166152008	4003479664
Total length (>= 25000 bp)	3119711632	3550261715	3452967778	3897289116
Total length (>= 50000 bp)	2400080225	3275969678	2647693108	3704640383
# contigs	112527	33035	110135	24184
Largest contig	2170611	5276269	2753427	8967193
Total length	4046355081	3733314870	4336770215	4008351139
GC (%)	42.89	42.57	43.17	42.84
N50	74514	325701	78564	514031
N90	14295	41727	15962	65625
auN	172736.7	608980.5	189833.9	874464.1
L50	10897	2542	10934	1844
L90	65455	15577	64363	10408
# N's per 100 kbp	0	0	0	0