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Thanks for this great tool! However, I have a few questions on input for cobra
1. Now I'm using megahit to assembly (I just know from #3 that it may generate many chimeric contigs, but spades may r…
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Hi,
I would like to keep chromosomes of one of my genomes in the alignment in their original order but even with the -Q and -R options mummer seems to be coming up with its own order. Does anyone kno…
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We just found some unusal genomes yesterday : like achromobacter_xylosoxidans_01/SAMN12335635 and acinetobacter_baylyi/SAMEA6124625... these genemes share almost no k-mer with others of the same speci…
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Hi, everyone:
I am running docker/singularity version of MitoHiFi with apptainer as:
`apptainer run -C -B /home -B /project -B /scratch -W ${SLURM_TMPDIR} mitohifi.sif python3 /opt/MitoHiFi/src/…
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I will use for some analysis to know where the associated contigs mapped to on the primary. The begin and the end of an associated contig can be fully specified by the nodes in the string graph. We c…
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GenBank is already there, EBML should be supported as well.
We might also consider FASTA exports of contigs/CDS.
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for chrom in range (1,26): # 1..25
X, Y are skipped... please correct and generate new results
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Contigs were created by minia with max contig length 16091 nt. When these contigs (fasta) were used as input to Ray 2.1.0 along with other PE and SE reads (fastq), Ray exited with segmentation error. …
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Is this possible?
For example, imagine a segmented virus. And I want to get the coverage for all segments.
Do I have to run the tool multiple times for each contig ID. Or might it be possible t…
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Hi,
First, thanks for developing LJA!
I am trying to run LJA on my HiFi data, using the command:
`lja -o lja_defPars --diploid -t 30 --reads hifi.fastq.gz`
The program crashes at the "Expor…