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Laura's user avatar
Laura
  • Member for 4 years, 10 months
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6 votes
1 answer
132 views

Is there a way to assemble contigs starting from a specific sequence?

3 votes
2 answers
723 views

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

3 votes
1 answer
335 views

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

3 votes
2 answers
401 views

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

2 votes
2 answers
193 views

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

2 votes
1 answer
70 views

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

2 votes
1 answer
37 views

Which non-matching DNA bases clash the least?

2 votes
2 answers
93 views

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

2 votes
1 answer
35 views

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

2 votes
1 answer
39 views

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

2 votes
0 answers
105 views

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

2 votes
2 answers
308 views

Is this a complete bacterial genome? (CheckM)

2 votes
2 answers
71 views

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

2 votes
2 answers
65 views

Software for taxonomic assignment?

2 votes
6 answers
3k views

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

2 votes
1 answer
400 views

How to edit the headers of multiple fasta files from multiple folders?

2 votes
1 answer
2k views

Fasterq-dump: --split-spot or -concatenate-reads?

2 votes
2 answers
303 views

How to download multiple proteomes at once?

1 vote
1 answer
233 views

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

1 vote
1 answer
91 views

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

1 vote
0 answers
37 views

Gene Ontology equivalent - higher specificity?

1 vote
1 answer
204 views

Phylogenetics software that can represent collapsed nodes as triangles

1 vote
1 answer
184 views

Comparing gene abundances between metagenomes

1 vote
1 answer
59 views

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

1 vote
0 answers
260 views

How to use SRA Toolkit to blast SRA accessions?

1 vote
0 answers
114 views

Prokka + table2asn (NCBI submission)

1 vote
1 answer
62 views

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

1 vote
1 answer
62 views

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

1 vote
2 answers
148 views

Is there an equivalent of Entrez queries for local BLAST?

0 votes
2 answers
98 views

What are some ways to check metagenomic bin quality?