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I tried to follow the usage example outlined at https://dib-lab.github.io/kSpider/, but the instructions no longer work. Specifically, the indexing step seems to have changed from `kSpider index_kmers…
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The faidx for my largest chromosome in the original assembly is as follows:
Chr1 196345723 6 60 61
The faidx for rawMask_35.fa and mask_35_50.fa show the following:
Chr1 …
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Thank you for the nice and very efficient assembler.
I assembled a highly heterozygous genome and hifiasm did very well separating primary and haplotigs (p_ctg size is only a bit larger than the ex…
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In my assembler `shovill` i estimate the genome size from kmer frequencies and use that to subsample the reads to a fixed coverage (100x) much like rasusa does:
https://github.com/tseemann/shovill/…
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The worst offender right now is interval 13913 in the current data set:
13913 Y:16691826-16692366 hdfs://svdev-1-m:8020/user/cwhelan/outs_tws_kill_promiscuous_kmers/NA12878_PCR-_30X/fastq/assem…
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Hello,
I'm very excited to test and assess the quality of our phased assembly (FALCON-Unzip -> FALCON-Phase).
However due to the nature of our system we are unable to acquire the parents of our sequ…
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Currently workflow does k-mer counting on the individual fastqs from each bam, but then goes on to combine the fastq. Should k-mer counting be performed on the combined fastq or the parts?
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Example:
- `{batch}.samples.tsv`
Example from previous pipelines:
```
sample asm_fn asm_ns asm_cl asm_fa_bytes pre_fn pre_ns pre_cl pre_kmers pre_fa_bytes baps_order mashtree_order…
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Hi, Thank you for developing a useful tool. I have run Nanocompore with my data but I got the following error.
```
PLEASE NOTE: This is an experimental module to load a centrally installed
minico…
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```
Here is my simple test to run your BSMAP. Could you tell me why
"Segmentation fault" happened?
bsmap -a t1.fa -d t1.fa -o t1_test
t1.fa
-------------------------------------------------
>1
TTATT…