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### Description of feature
Hi,
In the host removal module, the bowtie index needs to be recomputed from `--host_fasta` for each execution.
Would it be possible to add `--host_bt2` or similar to p…
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Is there a way to increase the visibility of SNPs at wider views? In the example below, I can see SNP differences between alignments in a 56 kb window, but not in a 140 kb window, which encompasses th…
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Hi Kraken2 developers/community,
I recently built a large Kraken2 database with genomes from the NCBI RefSeq database. I added genomes regardless of assembly level and limited it to 1 assembly per …
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Hello
I want to assemble all possible genomes . I need to align my reads against large database containing multiple reference genomes and assemble all possible genomes. is that possible with minYS?…
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Hi
We assemble the genome in hic mode and run the command as `hifiasm -o NA12878.asm -t 40 --h1 read1.fq.gz --h2 read2.fq.gz HiFi-reads.fq.gz`
Unfortunately, the size of `NA12878.asm.hic.h…
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There's quite a bit of interest https://github.com/sourmash-bio/sourmash/issues/2816 https://github.com/sourmash-bio/sourmash/issues/3070 https://github.com/sourmash-bio/sourmash/issues/3089 in using…
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Hi!
I am running ISEScan on a large set of genome assemblies (consisting primarily of assemblies from Illumina data and a couple PacBio genome assemblies). The tools runs great on the test data and m…
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I'm trying to run this on my computer with a large FASTQ input file, and am running it as a subprocess in Python:
# # Set the desired parameters
kmer_size = 31
genome_size = 2000000000
error_rat…
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Hi,
I am trying to build a database from RefSeq and GenBank genomes.
The total size of the ~1.9 million compressed genomes is ~8.5T. Since the data set contains many genomes, some of which with ex…
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Dear developers,
Thanks for your great software!
I am working on assembling a putative hexaploid or octoploid plant genome with a genome size of ~1.45 Gb by flow cytometry. In addition, the only…