Hi, i ran `nf-core/bacass`with illumina short reads as follows:

nextflow run nf-core/bacass \
-r 2.0.0 \
--input samplesheet.csv \
-profile singularity \
--skip_kraken2 \
--outdir ./results_bacass_v200 \
-resume

This produces a genome assembly with

Unicycler

that consists of multiple contigs (118 in my case). Is there a way to produce only 1 single contig? I want to use a provided reference genome to map the assembled genome to the reference and call

SNP

with Sarek after. If i have the different contigs it messes with the variant calling and considers every contig as a chromosome.

hi @Leon Hornich, Currently, there's no implemented feature in the nf-core/bacass pipeline that generates a single contig. The production of a single contig is a rare outcome and depends heavily on the complexity of the genome you're assembling. While some tools can help reduce the number of contigs, they are not yet integrated into this pipeline. Achieving a single contig, especially with short-read assemblies like Illumina, is challenging and uncommon without long-read data...

Hi @Daniel_VM, thank you a lot for the answer. Do you maybe know of a tool that attempts that? I am planning to do variant calling with the assembled genome and it would be useful to have a single sequence for that. If not i will figure out a alternative solution

I don’t know, sorry😵‍💫 . However, if you find one that improves the assembly, please feel free to create an issue to the nf-core/bacass repo 🙂. There has been some discussion about strategies to enhance assemblies, but they involve tools that haven't been implemented in nf-core/bacass yet. See issue#57

Still thanks for the help, i will open an issue in case i find something interesting 😄 For now i want to try if running

Unicycler

in

--mode bold

does anything. Probably not but it might be worth a shot 🤔