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8
votes
10
replies
9.5k
views
ANI calculation: alternatives to Jspecies
ani jspecies
updated 22 months ago by 7.1k • written 9.8 years ago by ▴ 620
17
votes
10
replies
8.6k
views
Bash loop using Edirect (esearch|efetch)
edirect esearch while
updated 3.0 years ago by 55k • written 8.3 years ago by ▴ 620
2
votes
1
reply
728
views
How to plot a mutation barplot of the SARS-CoV-2 genome?
seaborn python sars-cov-2 R
3.1 years ago by fhsantanna ▴ 620
1
vote
0
replies
728
views
Answer: Answer: How to plot a mutation barplot of the SARS-CoV-2 genome?
3.1 years ago by fhsantanna ▴ 620
0
votes
0
replies
1.1k
views
Comment: Comment: Generate consensus from a BAM file to each of the variants
3.6 years ago by fhsantanna ▴ 620
0
votes
0
replies
1.1k
views
Comment: Comment: Generate consensus from a BAM file to each of the variants
3.6 years ago by fhsantanna ▴ 620
2
votes
3
replies
1.1k
views
Generate consensus from a BAM file to each of the variants
bam coinfection consensus ivar
3.6 years ago by fhsantanna ▴ 620
0
votes
0
replies
2.2k
views
Comment: Comment: What is the error of this Nexus file? I cannot open it in Figtree
3.9 years ago by fhsantanna ▴ 620
0
votes
3
replies
2.2k
views
What is the error of this Nexus file? I cannot open it in Figtree
figtree ggtree R phylogenetics
3.9 years ago by fhsantanna ▴ 620
0
votes
0
replies
758
views
Color nexus tree automatically using associated data
nexus ape ggtree R python
3.9 years ago by fhsantanna ▴ 620
0
votes
0
replies
799
views
How to subsample SARS-CoV-2 dataset with limited computational resources?
sars-cov-2 subsample ram genome gisaid
4.0 years ago by fhsantanna ▴ 620
1
vote
0
replies
3.3k
views
Answer: A: Trimming reads using ivar - assembly of sars-cov-2 genome
4.1 years ago by fhsantanna ▴ 620
1
vote
5
replies
3.3k
views
Trimming reads using ivar - assembly of sars-cov-2 genome
ivar trimming sars-cov-2
4.1 years ago by fhsantanna ▴ 620
0
votes
0
replies
3.3k
views
Comment: C: Trimming reads using ivar - assembly of sars-cov-2 genome
4.2 years ago by fhsantanna ▴ 620
0
votes
0
replies
3.3k
views
Comment: C: Trimming reads using ivar - assembly of sars-cov-2 genome
4.2 years ago by fhsantanna ▴ 620
3
votes
2
replies
1.5k
views
Are phylogenetic reconstruction methods considered machine-learning approaches?
machine learning phylogeny
written 5.6 years ago by ▴ 620
0
votes
1
reply
1.9k
views
Comment: C: Protocol for genome assembly of Sars-cov-2 sequences
4.6 years ago by fhsantanna ▴ 620
0
votes
0
replies
1.9k
views
Comment: C: Protocol for genome assembly of Sars-cov-2 sequences
4.6 years ago by fhsantanna ▴ 620
4
votes
6
replies
1.9k
views
Protocol for genome assembly of Sars-cov-2 sequences
sars sars-cov-2 genome Assembly
updated 4.6 years ago by 149k • written 4.6 years ago by ▴ 620
0
votes
0
replies
635
views
Color genes/proteins based on taxonomic best-hit (bacterial genome)
hgt thermophiles bacteria genome plot
4.8 years ago by fhsantanna ▴ 620
3
votes
9
replies
3.7k
views
Blast in metagenomics: should I download all NR database for this purpose?
metagenomics blast local
updated 5.1 years ago by ▴ 330 • written 8.4 years ago by ▴ 620
0
votes
1
reply
5.9k
views
Comment: A: MEGAN5 - input blast -m8 option problem
updated 5.1 years ago by 44k • written 10.7 years ago by ▴ 620
0
votes
0
replies
2.5k
views
Comment: C: Reduce redundancy of alignment based on taxonomy and identity
updated 5.1 years ago by 44k • written 9.1 years ago by ▴ 620
3
votes
6
replies
7.0k
views
Compute a identity matrix from an alignment - command line approach for batch processing
alignment identity batch
updated 5.4 years ago by • 0 • written 8.1 years ago by ▴ 620
0
votes
1
reply
887
views
What is the difference between binning and phylotyping?
binning phylotyping metagenomics
5.5 years ago by fhsantanna ▴ 620
0
votes
0
replies
1.5k
views
Comment: C: Are phylogenetic reconstruction methods considered machine-learning approaches?
5.6 years ago by fhsantanna ▴ 620
1
vote
0
replies
3.5k
views
Comment: C: gbk2faa: why is it not working for refseq gbk?
5.6 years ago by fhsantanna ▴ 620
0
votes
0
replies
1.9k
views
Comment: C: Speed up psiblast of 11k alignments
5.6 years ago by fhsantanna ▴ 620
1
vote
6
replies
1.9k
views
Speed up psiblast of 11k alignments
psiblast parallel
updated 5.6 years ago by 20 • written 5.7 years ago by ▴ 620
0
votes
2
replies
1.9k
views
Comment: C: Speed up psiblast of 11k alignments
5.7 years ago by fhsantanna ▴ 620
5
votes
8
replies
2.4k
views
Getting proteins from genomic interval of a genbank file
genbank proteins cds biopython
updated 5.8 years ago by 22k • written 5.8 years ago by ▴ 620
0
votes
1
reply
2.4k
views
Comment: C: Getting proteins from genomic interval of a genbank file
5.8 years ago by fhsantanna ▴ 620
0
votes
0
replies
2.4k
views
Comment: C: Getting proteins from genomic interval of a genbank file
5.8 years ago by fhsantanna ▴ 620
0
votes
1
reply
2.4k
views
Comment: C: Getting proteins from genomic interval of a genbank file
5.8 years ago by fhsantanna ▴ 620
0
votes
0
replies
2.4k
views
Comment: C: Getting proteins from genomic interval of a genbank file
5.8 years ago by fhsantanna ▴ 620
1
vote
2
replies
933
views
Gene context metrics: software/algorithm
gene context neighborhood
5.9 years ago by fhsantanna ▴ 620
0
votes
0
replies
933
views
Comment: C: Gene context metrics: software/algorithm
5.9 years ago by fhsantanna ▴ 620
0
votes
0
replies
15k
views
Comment: C: How to count the length of fasta sequences?
5.9 years ago by fhsantanna ▴ 620
0
votes
1
reply
15k
views
Answer: A: How to count the length of fasta sequences?
5.9 years ago by fhsantanna ▴ 620
12
votes
10
replies
11k
views
6 follow
Criteria for filtering contigs after spades assembly
spades Assembly contigs filtering
updated 5.9 years ago by • 0 • written 7.1 years ago by ▴ 620
15
votes
9
replies
13k
views
7 follow
How do I access genome coverage using SPADES?
SPADES genome coverage
updated 2.4 years ago by 44k • written 9.5 years ago by ▴ 620
9
votes
6
replies
8.6k
views
How to recover a 16S rRNA gene from genome reads?
rRNA genome denovo assembly
updated 6.3 years ago by ▴ 20 • written 7.9 years ago by ▴ 620
2
votes
2
replies
1.7k
views
Software to group full length 16S rRNA sequences based on identity threshold
rRNA 16S identity matrix species
updated 6.6 years ago by ★ 3.3k • written 6.6 years ago by ▴ 620
2
votes
2
replies
3.3k
views
Evaluating the quality of draft genomes: checkm vs reapr
checkm reapr draft-genome
updated 2.9 years ago by 44k • written 10.1 years ago by ▴ 620
47
votes
13
replies
17k
views
13 follow
Best software to assemble bacterial genomes
illumina assembler assembly bacteria
updated 3.0 years ago by 44k • written 10.3 years ago by ▴ 620
0
votes
1
reply
11k
views
Comment: C: Criteria for filtering contigs after spades assembly
7.1 years ago by fhsantanna ▴ 620
0
votes
0
replies
11k
views
Comment: C: Criteria for filtering contigs after spades assembly
7.1 years ago by fhsantanna ▴ 620
0
votes
0
replies
11k
views
Comment: C: Criteria for filtering contigs after spades assembly
7.1 years ago by fhsantanna ▴ 620
0
votes
0
replies
3.6k
views
Answer: A: Make motif position matrix based on multiple sequence alignment.
7.7 years ago by fhsantanna ▴ 620
0
votes
0
replies
8.6k
views
Comment: C: How to recover a 16S rRNA gene from genome reads?
7.9 years ago by fhsantanna ▴ 620
161 results • Page 1 of 4
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