Xi Chen

inconsistent `ms` scores

3

Hi, When aligning a sequence to an augmented reference database I got a different `ms`, I wonder does `ms` depend on `tp`? One reference seq: ```bash minimap2 -cx map-ont one.fa...

possibility of removing secondary alignments that are actually supplementary (chimera)?

1

Hi, I noticed that if the primary alignment is chimeric (multiple tp:A:P tags) and say one or multiple pieces of the alignment has a low alignment score (ms or AS...

v2.1.9 does not output `send` correctly when using long-read mode

4

v2.1.8: ``` diamond blastx -q GCF_000708165.1_E_coli_EC2.contigs_genomic.fna -d a.fasta --range-culling -F15 --outfmt 6 qseqid sseqid sstart send scovhsp NZ_JFJL01000045.1 WP_000046661.1 1 109 100 ``` v2.1.9: ``` diamond blastx -q GCF_000708165.1_E_coli_EC2.contigs_genomic.fna -d...

random output using long read mode

1

Hi, I noticed that sometime the results is not reproducible using the long read mode, I wonder is it related to the internal seed or tie breaking? Here is a...

Is it safe to run genomad directly on nanopore R10.4.1 long reads?

1

Hi, Thanks for providing genomad, it is very useful. I was wondering would it be OK to run genomad directly on raw nanopore reads (>1000 bp, median q19) instead of...

Saved models could not be loaded: 'str' object has no attribute 'decode'

7

The installed checkm2 v1.0.1 returns an error saying that the model could not be loaded. `testrun` seems not working. Manual installation with checkm2 v1.0.2 by `git clone` and `python setup...

[feature request] seqkit subseq with --circular option?

4

Hi Wei, I wonder would it be possible to add a `--circular` option also to `seqkit subset`? I am currently using `seqkit subset` to extract the flanking regions of some...

plasmid classified as virus?

7

Hi, When classifying some Refseq sequences I noticed that some plasmids are being classified as virus. For example the reference assembly of Klebsiella pneumoniae (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000240185.1/). It seems sequence NC_016838.1 has...

fastq input raises error for `diamond v2.1.11`

1

`diamond v2.1.11` raises error on fastq files (https://github.com/bbuchfink/diamond/issues/855). Downgrading `diamond` to `v2.1.10` or converting fastq files to fasta (`seqkit fq2fa`) solves the issue.

The tar file seems corrupted? https://arken.nmbu.no/~larssn/humgut/HumGut2.tar.gz ``` ... fna/GUT_GENOME109309.fna.gz fna/GUT_GENOME286501.fna.gz fna/GCF_000701665.1_ASM70166v1_genomic.fna.gz gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is...