-
Hi, basalt developer,
BASALT is great. I have two technique questions.
1, what is the threshold of dRep used in the pipeline?
In the paper and the read.me, we could read dRep strategy wer…
-
Hi,
I have several assembled TCR chain contigs in a file, such as:
> tig1
TACAGATAG....
> tig2
TACAGATAG....
> tig3
TACAGATAG....
After trust4 gene assignments, I discovered the outputs in t…
-
crunching numbers on contig-level stats in #73 I get --
strict:
ContigInfo.NO_IDENT 120035 contigs / 599.6 Mbp
ContigInfo.CLEAN 109778 contigs / 1193.3 Mbp
ContigInfo.NO_HASH 6079 contigs / 19.0…
-
Hi Chong,
I'am from France and I think I have some problems with TERefiner_1. I wanted to know is it important for the rest of my analyzes? I obtain my contigs.fa but after Scaffolding I have zero …
-
It would be nice to wrap up information about the length of each contig and the IDs associated with it in a single object.
Use case:
```
chr1 = ensembl.contig(1)
covered_by_exons = np.zeros(len(chr…
-
numbers from contig-level stats in #73 --
```
strict reasons:
3 2076 contigs / 14.6 Mbp
1 1355 contigs / 11.5 Mbp
2 196 contigs / 1.8 Mbp
relaxed reasons:
3 2618 contigs / 18.3 Mbp
1 1681 …
-
Hi Haoyu,
Thank you so much for developing this amazing tool that enables the haplotype-resolved genome assembly.
Previous studies show that hifiasm can successfully seperate X and Y contigs in…
-
Hello. I ran purge_dups successfully up through (including) the get_seqs step. See results from my slurm output file below. Both .hap.fa and .purged.fa files were produced but they are smaller than wh…
-
[extract-max-extent-around-hashes.py](https://github.com/ctb/2022-sourmash-sens-spec/blob/main/scripts/extract-max-extent-around-hashes.py) is a potentially useful script that does the following:
G…
-
Hi Ryan,
Thanks for writing Unicycler, it is a very useful tool.
I ran a hybrid assembly using conservative mode (same result for normal mode) and I obtained 3 contigs, as follows:
>1 length=41…