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Hi All,
I am new to bioinformatics, self-learning as I go and have limited knowledge in it. I am trying to assembly an E. coli genome using Illumina reads and ONT reads. I was able to assemble 2 ou…
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Hello,
I have the following issue with AlignGraph: the program crashes during the creation of _short_initial_contigs_extended_contigs.* files by BLAT (corresponding to that line of code: s = "blat …
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Dear author
The valueError was occurred when we used the DRAM-v.py to annotate our data.
Can you provide the method to correct the error?
We will appreciated for this
Traceback (most r…
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Hi, thanks for your very useful tool, and the one I am using it version 1.9.0. I have extracted viral contigs from metagenomic sequencing data of stool, and now want to estimate the relative abundance…
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A useful feature could be to label contigs based on other columns than the sequence ID. e.g. the 16S rRNA gene classification of a contig.
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Sometimes, the IVA assembler can't assemble one large contig, but it assembles several smaller contigs that either have small gaps between them or have some overlap.
For example, 73060A-HCV_S46 fro…
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I'm using getorganelle to extract mitochondrial genomes from insects. I first do an assembly using SPAdes (because we use that output for other downstream tasks anyway), and then I run get_organelle_f…
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I am attempting to use quickmerge in an attempt to merge contigs from a long-read assembly into chromosome-length scaffolds using the hg38 reference genome. Please see the example command below:
me…
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Hello
I have two viral contigs of approximately 3500bp from the same region of a genome. The two contigs differ by just 1%. Virsorter is run as:
virsorter run -w test.out -i test.fa --min-length 150…
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Hello Dr. Li,
I have been processing TCR data in single cells recently. I observed from the TRUST4 output file that the numbers after the barcode are not as ordered as 0123.
CATCGAAGTTAGGGTG_0 0 TR…