User Laura

1 vote

1 answer

62 views

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

asked Sep 21, 2023 at 15:37

1 vote

1 answer

65 views

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

asked Aug 28, 2023 at 10:34

1 vote

0 answers

143 views

Prokka + table2asn (NCBI submission)

asked May 31, 2023 at 15:49

2 votes

2 answers

110 views

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

asked May 11, 2023 at 9:37

2 votes

1 answer

37 views

Which non-matching DNA bases clash the least?

asked Mar 6, 2023 at 11:17

2 votes

1 answer

74 views

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

asked Feb 24, 2023 at 10:23

2 votes

2 answers

205 views

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

asked Jan 9, 2023 at 12:48

1 vote

2 answers

165 views

Is there an equivalent of Entrez queries for local BLAST?

asked Oct 11, 2022 at 10:30

3 votes

2 answers

417 views

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

asked Oct 6, 2022 at 16:00

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?

asked Jun 29, 2022 at 9:39

2 votes

1 answer

36 views

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

asked Jun 16, 2022 at 6:44

1 vote

1 answer

60 views

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

asked Jun 8, 2022 at 14:23

2 votes

2 answers

76 views

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

asked May 25, 2022 at 12:03

2 votes

2 answers

353 views

Is this a complete bacterial genome? (CheckM)

asked Feb 14, 2022 at 10:53

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?

asked Jan 16, 2022 at 8:40

0 votes

2 answers

101 views

What are some ways to check metagenomic bin quality?

asked Dec 3, 2021 at 14:10

1 vote

0 answers

271 views

How to use SRA Toolkit to blast SRA accessions?

asked Aug 4, 2021 at 12:27

3 votes

1 answer

375 views

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

asked Dec 10, 2020 at 16:13

0 votes

1 answer

27 views

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

asked Nov 25, 2020 at 16:51

0 votes

1 answer

29 views

Comparing groups of 16S rRNA sequences - how to?

asked Oct 1, 2020 at 10:07

2 votes

6 answers

3k views

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

asked Sep 1, 2020 at 9:42

2 votes

2 answers

65 views

Software for taxonomic assignment?

asked Aug 12, 2020 at 14:39

0 votes

2 answers

231 views

Using variables with fasterq-dump?

asked Aug 5, 2020 at 10:06

1 vote

1 answer

193 views

Comparing gene abundances between metagenomes

asked Jul 6, 2020 at 11:00

1 vote

1 answer

212 views

Phylogenetics software that can represent collapsed nodes as triangles

asked May 21, 2020 at 12:25

1 vote

0 answers

37 views

Gene Ontology equivalent - higher specificity?

asked May 13, 2020 at 14:28

3 votes

2 answers

747 views

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

asked Apr 3, 2020 at 11:31

1 vote

1 answer

251 views

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

asked Mar 17, 2020 at 16:35

2 votes

2 answers

322 views

How to download multiple proteomes at once?

asked Feb 24, 2020 at 17:14

0 votes

1 answer

234 views

Can I get longer contigs by changing MEGAHIT settings?

asked Feb 20, 2020 at 17:48

Stack Exchange Network

35 Questions

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

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

Prokka + table2asn (NCBI submission)

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

Which non-matching DNA bases clash the least?

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

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

Is there an equivalent of Entrez queries for local BLAST?

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

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

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

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

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

Is this a complete bacterial genome? (CheckM)

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

What are some ways to check metagenomic bin quality?

How to use SRA Toolkit to blast SRA accessions?

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

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

Comparing groups of 16S rRNA sequences - how to?

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

Software for taxonomic assignment?

Using variables with fasterq-dump?

Comparing gene abundances between metagenomes

Phylogenetics software that can represent collapsed nodes as triangles

Gene Ontology equivalent - higher specificity?

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

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

How to download multiple proteomes at once?

Can I get longer contigs by changing MEGAHIT settings?