User: benv

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benv710
Reputation:
710
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Trusted
Location:
Canada
Last seen:
2 weeks, 2 days ago
Joined:
3 years, 9 months ago
Email:
b***@bcgsc.ca

Posts by benv

<prev • 79 results • page 1 of 8 • next >
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Answer: A: Make error for abyss-PE with many libraries
... Hi @ck178807, Your `abyss-pe` command looks good in principle. Your problem has something to do with the newlines and line continuations ("\" characters) in your command. I sometimes struggle with this myself. Please try collapsing your command line into a single line, confirm that it fixes the ...
written 4 weeks ago by benv710
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Comment: C: ABySS min = 500 ; how to change it
... That is exactly right, @h.mon. The 500 bp length threshold is only used by `abyss-fac` when calculating contiguity stats (e.g. N50). (`abyss-fac` has a `-t` option for changing the threshold, which defaults to 500 bp.) The output assembly FASTA files from ABySS are never filtered by sequence lengt ...
written 7 weeks ago by benv710
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Answer: A: How does the memory requirements of abyss scale ?
... @lieven.sterck, You have the right idea with respect to distinct k-mers -- the memory usage of ABySS is linear w.r.t. the number of distinct k-mers in the input reads. The number of distinct k-mers in the data set depends jointly on: (i) genome size, (ii) sequencing error rate (sequencing errors c ...
written 8 months ago by benv710
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Answer: A: Is the Abyss contig and scaffold phased?
... Hi James, No, ABySS does not attempt to create a phased assembly. Like most de novo genome assemblers, it is a haploid assembler (it collapses heterozygous regions into a consensus). W.r.t. to your contig alignments in IGV, it is normal to see pileups in repeat regions, but you generally should no ...
written 9 months ago by benv710
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Comment: C: unrecognized error in the abyss assembly software
... I'm not a Conda user, but it appears that you have a version mismatch between the installed versions of ABySS and gcc (libgomp is a part of gcc that implements multithreading.) In other words, ABySS was compiled with some other version of gcc (libgomp) than what is installed in Conda. I noticed th ...
written 9 months ago by benv710
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Comment: C: SNP calling from a scaffold.fa file
... Thanks, @pfs! I was just about to suggest the same. ...
written 10 months ago by benv710
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Comment: C: Reading single-end reads takes forever
... Sorry for slow response. To run a single-end assembly only, specify the input single-end reads with `se=""` or `in=""` and add the word "unitigs" to the end of the `abyss-pe` command. ...
written 12 months ago by benv710
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Comment: C: ABySS and Velvet "number of contigs and contig length in pair-end and single-en
... I am not familiar with Velvet usage, but if you provide the `abyss-pe` command and verbose log output (add "v=-v" to `abyss-pe` command), I could have a look. Output of `abyss-fac` (N50 etc.) is helpful as well. It is standard practice to run assemblies for a range of k-mer sizes to achieve the be ...
written 12 months ago by benv710
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Comment: C: Bosst configure error
... It is really hard to tell what is wrong from the `configure` output alone. If you look for the Boost checks in the `config.log` file it will give you more info about why the checks failed. If you like, you can post your config.log (post here, send e-mail to benv at bcgsc dot ca, or post to GitHub ...
written 13 months ago by benv710
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Comment: C: Rescaffolding a genome assembly?
... Good to know. Thanks for posting back! ...
written 13 months ago by benv710

Latest awards to benv

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 8 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 13 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 14 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 14 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Appreciated 18 months ago, created a post with more than 5 votes. For A: Reading single-end reads takes forever
Scholar 18 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 18 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 18 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 18 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 2.6 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
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Scholar 2.9 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 2.9 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 2.9 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3.0 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3.5 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS

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