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8
votes
10
replies
8.7k
views
ANI calculation: alternatives to Jspecies
ani jspecies
updated 12 months ago by 6.4k • written 9.0 years ago by ▴ 620
17
votes
10
replies
7.9k
views
Bash loop using Edirect (esearch|efetch)
edirect esearch while
updated 2.2 years ago by 54k • written 7.6 years ago by ▴ 620
2
votes
1
reply
557
views
How to plot a mutation barplot of the SARS-CoV-2 genome?
seaborn python sars-cov-2 R
2.4 years ago by fhsantanna ▴ 620
2
votes
3
replies
889
views
Generate consensus from a BAM file to each of the variants
bam coinfection consensus ivar
2.8 years ago by fhsantanna ▴ 620
0
votes
3
replies
1.9k
views
What is the error of this Nexus file? I cannot open it in Figtree
figtree ggtree R phylogenetics
3.2 years ago by fhsantanna ▴ 620
0
votes
0
replies
635
views
Color nexus tree automatically using associated data
nexus ape ggtree R python
3.2 years ago by fhsantanna ▴ 620
0
votes
0
replies
697
views
How to subsample SARS-CoV-2 dataset with limited computational resources?
sars-cov-2 subsample ram genome gisaid
3.2 years ago by fhsantanna ▴ 620
1
vote
5
replies
2.9k
views
Trimming reads using ivar - assembly of sars-cov-2 genome
ivar trimming sars-cov-2
3.4 years ago by fhsantanna ▴ 620
3
votes
2
replies
1.3k
views
Are phylogenetic reconstruction methods considered machine-learning approaches?
machine learning phylogeny
written 4.9 years ago by ▴ 620
4
votes
6
replies
1.6k
views
Protocol for genome assembly of Sars-cov-2 sequences
sars sars-cov-2 genome Assembly
updated 3.9 years ago by 142k • written 3.9 years ago by ▴ 620
0
votes
0
replies
550
views
Color genes/proteins based on taxonomic best-hit (bacterial genome)
hgt thermophiles bacteria genome plot
4.0 years ago by fhsantanna ▴ 620
3
votes
9
replies
3.3k
views
Blast in metagenomics: should I download all NR database for this purpose?
metagenomics blast local
updated 4.3 years ago by ▴ 330 • written 7.6 years ago by ▴ 620
3
votes
6
replies
6.4k
views
Compute a identity matrix from an alignment - command line approach for batch processing
alignment identity batch
updated 4.7 years ago by • 0 • written 7.4 years ago by ▴ 620
0
votes
1
reply
752
views
What is the difference between binning and phylotyping?
binning phylotyping metagenomics
4.8 years ago by fhsantanna ▴ 620
1
vote
6
replies
1.6k
views
Speed up psiblast of 11k alignments
psiblast parallel
updated 4.9 years ago by 20 • written 5.0 years ago by ▴ 620
5
votes
8
replies
2.0k
views
Getting proteins from genomic interval of a genbank file
genbank proteins cds biopython
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 620
1
vote
2
replies
809
views
Gene context metrics: software/algorithm
gene context neighborhood
5.1 years ago by fhsantanna ▴ 620
12
votes
10
replies
9.4k
views
6 follow
Criteria for filtering contigs after spades assembly
spades Assembly contigs filtering
updated 5.2 years ago by • 0 • written 6.3 years ago by ▴ 620
15
votes
9
replies
12k
views
7 follow
How do I access genome coverage using SPADES?
SPADES genome coverage
updated 19 months ago by 43k • written 8.7 years ago by ▴ 620
9
votes
6
replies
7.7k
views
How to recover a 16S rRNA gene from genome reads?
rRNA genome denovo assembly
updated 5.6 years ago by ▴ 20 • written 7.1 years ago by ▴ 620
2
votes
2
replies
1.5k
views
Software to group full length 16S rRNA sequences based on identity threshold
rRNA 16S identity matrix species
updated 5.9 years ago by ★ 3.2k • written 5.9 years ago by ▴ 620
2
votes
2
replies
3.1k
views
Evaluating the quality of draft genomes: checkm vs reapr
checkm reapr draft-genome
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 620
47
votes
13
replies
16k
views
13 follow
Best software to assemble bacterial genomes
illumina assembler assembly bacteria
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 620
0
votes
1
reply
1.6k
views
Functional interpretation of a bacterial transcriptome
transcriptomics bacteria functional annotation
7.3 years ago by fhsantanna ▴ 620
6
votes
8
replies
2.6k
views
Metrics to evaluate tree congruence
phylogeny congruence software
updated 7.3 years ago by ★ 3.0k • written 7.4 years ago by ▴ 620
1
vote
5
replies
3.7k
views
De novo genome assembly using Ion Proton data: which assembler do you recommend?
ion-proton Assembly iontorrent
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 620
2
votes
2
replies
2.7k
views
Reapr perfectmap issue
verification perfectmap reapr
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 620
0
votes
2
replies
1.9k
views
Metagenomic Iontorrent reads: filtering and denoising
metagenome reads filtering denoise
updated 7.6 years ago by ★ 2.4k • written 7.6 years ago by ▴ 620
2
votes
13
replies
3.1k
views
DOOR2 (operon predictor) does not load my fna file, do you know an alternative software?
door2
7.9 years ago by fhsantanna ▴ 620
3
votes
5
replies
3.3k
views
How do I compile Quake (error correction of Miseq reads) in Ubuntu?
ubuntu quake error_correction compile
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 620
5
votes
11
replies
3.5k
views
All reads with mapq value <= 1, htseq does not attribute counts to any feature
rnaseq mapq
8.2 years ago by fhsantanna ▴ 620
9
votes
2
replies
2.4k
views
Incompatibility between bbmap and htseq?
bbmap htseq
updated 8.2 years ago by 142k • written 8.2 years ago by ▴ 620
3
votes
5
replies
3.2k
views
gbk2faa: why is it not working for refseq gbk?
biopython
updated 21 months ago by 43k • written 8.3 years ago by ▴ 620
1
vote
3
replies
2.3k
views
Reduce redundancy of alignment based on taxonomy and identity
CD-HIT alignment redundancy
8.3 years ago by fhsantanna ▴ 620
2
votes
3
replies
1.6k
views
Why some genomes are not available in genbank ftp?
genbank ftp
updated 9.0 years ago by 35k • written 9.0 years ago by ▴ 620
0
votes
1
reply
1.5k
views
Strategies to pare down alignment data
redundancy alignment phylogeny
updated 16 months ago by 43k • written 9.0 years ago by ▴ 620
27
votes
50
replies
18k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 15 months ago by 43k • written 9.0 years ago by ▴ 620
0
votes
3
replies
1.9k
views
Tblastx returning only 400 hits
tblastx artemis act
updated 15 months ago by 43k • written 9.1 years ago by ▴ 620
3
votes
4
replies
4.9k
views
How to create a Venn diagram using ortholog clusters?
get_homologues venn-diagram ortholog
updated 22 months ago by 43k • written 9.1 years ago by ▴ 620
8
votes
5
replies
2.2k
views
How get intervals of low coverage from a genome sequence?
interval low-coverage script
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 620
1
vote
1
reply
2.1k
views
Genbank submission error: ERROR: valid [SEQ_FEAT.CDSproductPackagingProblem] Protein product not packaged in nuc-prot set with nucleotide
error genbank submission genome
9.3 years ago by fhsantanna ▴ 620
1
vote
4
replies
2.6k
views
Software to display draft genome statistics
statistics genome proteins
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 620
14
votes
6
replies
6.6k
views
What are the best approaches to evaluate a genome assembly using the 'intrinsic' data?
assembly genome validation
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 620
2
votes
1
reply
2.1k
views
Spades assembler artifacts? Contigs containing long nt stretches.
artifacts contigs Assembly genome spades
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 620
3
votes
8
replies
4.3k
views
Metagenomic read recruitment: best software
read metagenomics recruitment
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 620
0
votes
1
reply
2.0k
views
Read recuitment: promer and artemis
promer metagenomics recruitment; artemis mummer
updated 3.1 years ago by 43k • written 9.6 years ago by ▴ 620
1
vote
3
replies
4.2k
views
get_homologues installation error: make: Nothing to be done for `all.
installation ubuntu get_homologues
updated 3.2 years ago by 43k • written 9.6 years ago by ▴ 620
1
vote
16
replies
5.3k
views
SEED assignment (MEGAN5)
BLAST RefSeq MEGAN5 metagenomics SEED
updated 2.4 years ago by 43k • written 9.9 years ago by ▴ 620
2
votes
2
replies
3.1k
views
Error loading blast table (outfmt 6 option) in Megan 5
metagenomics megan
updated 2.6 years ago by 43k • written 10.0 years ago by ▴ 620
3
votes
6
replies
5.5k
views
MEGAN5 - input blast -m8 option problem
metagenomics megan blast
updated 2.6 years ago by 43k • written 10.0 years ago by ▴ 620
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