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Should I consider contigs.fa or scaffolds.fa from SPAdes output for downstream analyses?

assembly spades quast contigs written 9 days ago by bioinforesearchquestions • 230 • updated 9 days ago by h.mon ♦ 26k

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141

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Quast shows different reads count for the same fastq file?

reads fastq contig quast written 11 weeks ago by DanielC • 80

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200

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Blog: Hacking QUAST and changing minimum allowed identity percentage setting

assembly tutorial quast genomics blog written 9 months ago by inaciogmedeiros • 10 • updated 9 months ago by h.mon ♦ 26k

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837

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Is there any alternative to QUAST software to evaluate de novo assembly results?

assembly quality evaluation quast written 16 months ago by oxfordsoccer • 10 • updated 16 months ago by Sej Modha ♦ 4.2k

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1.4k

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Tool for de novo assembly evaluation ??

soap quast written 3.2 years ago by Picasa • 420

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1.4k

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What is "Total Length" in QUAST?

quast written 3.4 years ago by ' • 170 • updated 3.4 years ago by thackl • 2.6k

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886

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traversal stats explanations

assembly contig quast traversal minia written 3.7 years ago by pbigbig • 190

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Recent Replies

A: Reads per COG normalization by Mensur Dlakic • 40
> Is there some way to normalize the number of reads mapped to each COG taken this information...
A: Megahit Assembly - command line error by Mensur Dlakic • 40
This part of your command **./megahit** means that you have a *megahit* executable in the present...
C: Reads per COG normalization by Asaf ♦ 5.9k
There are a lot of ways to normalize the data, the only question is why do you want to normalize it?
C: Megahit Assembly - command line error by Asaf ♦ 5.9k
Do you get an error?
C: limma voom - mean variance trend by furrdinand • 0
Yes, I used calcNormFactors with the TMM method prior to voom normalization on the dge object.
C: ABySS OpenMP version by SMK • 1.4k
No worries, updated by [https://www.biostars.org/u/23882/][1] already. [1]: https://www.biost...
A: How to find out human mtDNA genes in d-loop control region for Indian origin onl by grant.hovhannisyan • 1.6k
D-loop is a non-coding region, so it does not contain genes. Most probably you are looking for m...
C: Distinguishing between different formats for VCF file indexes by cmdcolin • 1.2k
Probably you can tell by the file extension. IDX is a "tribble index" and TBI is a tabix index
C: ABySS OpenMP version by SMK • 1.4k
You might need to edit the post (not to use the code chunk mode) to increase the readability.
A: Filtered a .vcf file based on id of a second file by cerriguglielmo • 0
Ok, the sample file contains the id while the file contains all data: The command that generate t...
C: How to do data cleaning for VCF genetic file by Shicheng Guo • 7.5k
the remaining task includes: Statistics: Alternative allele frequency > 0.5 sites: 3...
C: Unable to find FASTA index entry for 'unitig_2993_pilon error. by tmrhyd • 0
Nothing happened for either? the command didn't run a error, but didn't return any input either.

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