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Laura's user avatar
Laura's user avatar
Laura
  • Member for 5 years
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1 vote
1 answer
62 views

Using average of sequence similarities when delimiting genera - how to deal with outliers?

1 vote
1 answer
65 views

Variation in 16S rRNA between assemblers - how do I know which is real?

1 vote
0 answers
144 views

Prokka + table2asn (NCBI submission)

2 votes
2 answers
112 views

How to get the nucleotide sequence for protein NCBI accession code, programatically?

2 votes
1 answer
37 views

Which non-matching DNA bases clash the least?

2 votes
1 answer
74 views

Is there a graphical/interactive 16S rRNA clustering method?

2 votes
2 answers
205 views

Improving prokaryotic assembly with other contig/scaffold-level data?

1 vote
2 answers
165 views

Is there an equivalent of Entrez queries for local BLAST?

3 votes
2 answers
418 views

Remote blastn - what is breaking my (bash) loop?

2 votes
1 answer
41 views

How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?

2 votes
1 answer
36 views

rRNA genes missing from metagenomic bins; is there a way to recruit them?

1 vote
1 answer
60 views

Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

2 votes
2 answers
76 views

How can I improve or otherwise investigate an unreliable genome tree?

2 votes
2 answers
353 views

Is this a complete bacterial genome? (CheckM)

2 votes
0 answers
108 views

Does it make sense to compare the mean relative coverages for contigs / MAGs from samples that were not co-assembled?

0 votes
2 answers
101 views

What are some ways to check metagenomic bin quality?

1 vote
0 answers
272 views

How to use SRA Toolkit to blast SRA accessions?

3 votes
1 answer
380 views

What does the 'suppressed' folder mean on the NCBI ftp genomes website?

0 votes
1 answer
27 views

Is is possible to predict ncRNAs from sequence and homology alone?

0 votes
1 answer
29 views

Comparing groups of 16S rRNA sequences - how to?

2 votes
6 answers
3k views

How to measure the total size of a fastq file in base pairs?

2 votes
2 answers
65 views

Software for taxonomic assignment?

0 votes
2 answers
231 views

Using variables with fasterq-dump?

1 vote
1 answer
193 views

Comparing gene abundances between metagenomes

1 vote
1 answer
212 views

Phylogenetics software that can represent collapsed nodes as triangles

1 vote
0 answers
37 views

Gene Ontology equivalent - higher specificity?

3 votes
2 answers
747 views

Is there any value in scaffolding the output contigs of MEGAHIT assembler given a metagenomic dataset?

1 vote
1 answer
252 views

Will using smaller kmers help get larger contigs? If not, then what?

2 votes
2 answers
325 views

How to download multiple proteomes at once?

0 votes
1 answer
237 views

Can I get longer contigs by changing MEGAHIT settings?