Eric Edsinger

Using the length-evalue function for blast best hits (BH)

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Hi! crb-blast seems to work really great - I'm finding 17-39% improvement over blastp (both with default evalue cutoffs of 10-5) in identifying RBHs between de novo squid and pygmy...

Multiple transcripts to a single database protein in tsv output file

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Hi! I'm working with crb-blast for the first time and was able to use it without any obvious trouble (exit status 0) - running a query squid transcriptome against target...

Hi! I'm very interested / excited to try WENGAN out to assemble human-sized+ cephalopod genomes. I was wondering if there is a preset or recommended strategy for using WENGAN with...

Hi! I was wondering if there is a way to find out what specific parameters were used when OrthoFinder2 runs a piece of software, like Blastp. Also - is it...

Hi! I was wondering what you recommend for structuring sets of forward and reverse reads to provide to MAC when read length and insert size are variable. Our PE insert...

Using Illumina Hi-C and Chicago data?

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I have PACBIO SMRT Sequel data - and both Hi-C and Chicago Illumina data - but no standard PE or matepair Illumina data. Would you recommend using NextPolish with just...

Assembly is running around a month and going strong - or is it stalled?

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**Describe the bug** Unsure if assembly of octopus (human-sized) genome with 43x seed is active or stalled after running almost a month with 500 Gb RAM 60 CPU and 2...

Genome coverage inflection point for assembly quality (contig number and BUSCO)

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### Description of bug I am using Spades for genome assembly of Illumina PE data and while it runs great to completion on each job I've done, I'm finding there...

Does running iterations of quickmerge on quickmerge output create artifacts?

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I have multiple assemblies of hybrid and long-read sequencing. And its allowing me to run quickmerge on the output of quickmerge multiple times. I'm seeing increases in contig lengths and...

I have ONT only Shasta and Flye assemblies and dbg2olc and Masurca hybrid assemblies. I was wondering if there is a suggested strategy for merging them all with quickmerge. Is...