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Master tsv file for fist 1k assembler targets here:
[https://serratus-public.s3.amazonaws.com/rce/assembly/assembly_targets_first_1k.tsv](https://serratus-public.s3.amazonaws.com/rce/assembly/assem…
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Hi Alex,
I am trying to map my RNA-seq sequence to the virus genome. Since my genome size is around ~250K base long. So, I used `--genomeSAindexNbases 7` for building indices. Now, most of my samples…
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Hi guys!
We will be sequencing several hundred virus strains, and I am looking for a pipeline to do de-novo assembly and variant calling.
Since I have been working with nfcore @drpatelh in the…
ktrns updated
4 years ago
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I was running the latest version of Picard (v2.23.3) on some Influenza samples and ran into an issue because the sequence names contained parentheses which are no longer allowed in the SAM specificati…
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Thanks for this superb tool. I can see many uses.
I would love a walkthrough for producing an NCBI taxonomy with bacteria and archaea replaced with the GTDB hierarchy. In my case I only need a krak…
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![image](https://user-images.githubusercontent.com/9061708/30391941-1317ee0e-9870-11e7-8310-640dce99abc8.png)
The link to the download instructions brought me back to this for a full circle. Is th…
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Dear developers,
I have two quick questions.
1) will virnet work on the contigs with length greater than 2.5kb by using --input_dim=3000;
2) after running on my test file, I have problem to inter…
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I started working on this
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I used the following command to create a draft assembly for amplified cDNA from viral RNA
`/Linux-amd64/bin/canu -p HBV -d HBV-oxford contigFilter="2 0 1.0 0.5 0" genomeSize=3.2K -nanopore-raw /BC0…
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Thanks for the very nice tool! I performed the following command and came across an issue as below. `DRAM-v.py annotate -i viral.fasta -v VIRSorter_affi-contigs.tab -o test-cat1-annotation --min_cont…