Questions tagged [software-recommendation]

Questions asking whether a software exists for a certain purpose; questions asking which software is best among a selection for a certain purpose.

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

I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So ...
Laura's user avatar
  • 909
0 votes
1 answer
36 views

Bioprocess data visualisation and analysis

I'm looking for some kind of software, ideally FOSS, that will allow us to plot, compare, annotate and add additional points to time series data from bioprocessing runs (bioreactors). Many of the ...
Alext's user avatar
  • 1
3 votes
1 answer
130 views

Extract compounds/proteins from plant genomic data

I want a process by which I can identify genes within plant genomes; i.e. a process that works for all plants, not just for a single species. I'm wondering, if, by bioinformatic means only, it is ...
Sorin Trimbitas's user avatar
2 votes
1 answer
74 views

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

I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately. Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
Laura's user avatar
  • 909
1 vote
1 answer
90 views

Allele effects by parental-origin estimated from genotyping array data

We are dealing with relatively large family data (> 1,000 trios) with genotyping array data. We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...
PenguinPartyH0's user avatar
1 vote
0 answers
25 views

Recode bgen files against reference genome

I have a set of .bgen files split by chromosomes, including both SNPs and INDELS (named with both rsids and chr_pos_a1_a2). I know a large portion of them are encoded on the wrong strand, and I want ...
Giulio Centorame's user avatar
2 votes
0 answers
42 views

How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?

How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files? The way flow-jo exports is in wide rather than ...
Coo's user avatar
  • 131
0 votes
1 answer
125 views

Is there a software that allows to convert a jpeg graph into dataset?

I have a very old graph as a .jpeg picture that I would like to convert into a dataset to be able to operate with it using R/python. I have no idea if it is even possible.
Mark's user avatar
  • 103
2 votes
1 answer
114 views

Visualization of mutations in (part of) viral genome - existing tools?

I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info: but for individual sequences, probably on the base of the vcf files generated by the ARTIC ...
KeyboardCat's user avatar
0 votes
1 answer
505 views

How to de novo hybrid assemble with Pacbio CCS and Illumina PE reads

I would like to perform de novo genome assembly on a diploid microalgal strain. I have two datasets: PacBio CCS/HiFi reads, low coverage. Illumina PE 2x150 (standard shotgun) Does anybody have any ...
bishopia's user avatar
0 votes
1 answer
410 views

If I have data from a full genome sequence, how can I search for a known pathogenic variant of a known gene?

I have a CS background, but am a bioinformatics neophyte I did a full genome sequence which provided me with ~100GB of files (SNP VCF, Indel VCF, BAM, Indel TBI, SNP TBI, BAM BAI, CNV VCF, CNV TBI, CV ...
ensnare's user avatar
  • 101
1 vote
0 answers
728 views

How to get a consensus sequence from a nanopore fastq files?

I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed). I usually generate a consensus sequence with "...
Gerald Vasquez Aleman's user avatar
2 votes
0 answers
58 views

Which GWGAS Tool is 'better', MAGMA or LDSC?

I am currently doing a project regarding gene-based analysis and gene-set analysis given a certain GWAS dataset, I only know 2 well known gene-based analysis tool which is LDSC and MAGMA. As of now, I'...
Andreas Adinatha's user avatar
1 vote
2 answers
176 views

Finding SNP/Indel Markers of Interspecific Variation

This is a revised version of my original question, edited to include the portions already answered by @Maximilian Press. Goal: Find SNP and indel alleles which are fixed between but lack polymorphism ...
annabelperry's user avatar
0 votes
1 answer
27 views

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

I'm working with a set of homologous genes (let's call it gene A) from several bacterial species. I know (from previously published research) that in gene B (a close paralogue of gene A), there is a ...
Laura's user avatar
  • 909
2 votes
2 answers
311 views

How can I subset WGS data to the level of WES variants?

I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...
jared_mamrot's user avatar
0 votes
0 answers
477 views

MM/PB(GB)SA calculations for DESMOND trajectories

I did molecular dynamic simulations with DESMOND. Now, I want to obtain the interaction free energy using MM/PB(GB)SA. The free tools I found to perform such calculations are AmberTools and g_mmpbsa. ...
Camps's user avatar
  • 123
1 vote
0 answers
48 views

Is there a software that can predict protein-DNA binding?

Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
Anthony Guterres's user avatar
1 vote
0 answers
37 views

Gene Ontology equivalent - higher specificity?

I've recently discovered OrthoVenn2, which I'm using to compare proteomes and extract likely clade-specific genes. I'm enjoying software, and one of the things it offers is a breakdown of protein ...
Laura's user avatar
  • 909
2 votes
0 answers
342 views

Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!

I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data. I have the file contigs.fa from short reads but phasing step with ...
Enset's user avatar
  • 21
8 votes
2 answers
195 views

Understanding some of the computational bottlenecks of Covid-19 research

I am a researcher in high-performance computing (with very little bioinformatics background), and I am trying to understand what are the current biggest computational bottlenecks of software used for ...
Vincent's user avatar
  • 181
1 vote
3 answers
117 views

Software for microbial profiling from 16S rRNA gene sequence

I have hundreds of GBs metagenomic 16S rRNA gene sequence data. I want to do microbiome composition profiling (with relative abundance) from the data. Also after that, I will do functional profiling (...
DEEP's user avatar
  • 103
-1 votes
3 answers
258 views

Is it possible to do this in R?

I have a big clinical data file with 96 columns like age, gender, BMI, etc I want to see which of these clinical characteristics respond to chemotherapy. Response to chemotherapy divides patients to ...
Zizogolu's user avatar
  • 2,148
2 votes
3 answers
251 views

What assembler is appropriate for High-Fidelity PacBio reads

What assembler is appropriate for High-Fidelity PacBio reads? For example, canu is good for high-error PacBio reads. But what algorithm to use for HiFi reads? Would it be OK to use canu without the ...
Biomagician's user avatar
  • 2,459
1 vote
1 answer
449 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
marinegor's user avatar
2 votes
2 answers
439 views

How can I transform a mapped BAM file into an unmapped BAM file?

In order to use MergeBamAlignment (Picard), I need an unmapped BAM file and a mapped BAM file. I have two mapped BAM files: one with reads mapped to the reference I want but without metadata such as ...
Biomagician's user avatar
  • 2,459
1 vote
1 answer
39 views

Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment that will lead to the ...
Charles's user avatar
  • 537
3 votes
1 answer
101 views

Detecting broad peaks in sRNA-seq data

What kind of tool would be appropriate do detect "broad peaks" in small RNA-seq sequencing data? MACS2 appears to be developed for ChIP-seq data, but I see that there is a ...
bli's user avatar
  • 3,130
3 votes
1 answer
137 views

programmatic secondary structure prediction for >36-mer DNA oligonucleotides

I'm writing a tool to automate Sanger sequencing primer design for a production lab that uses a universal-tail chemistry Sanger sequencing to verify NGS results. Essentially, the template DNA is ...
mRotten's user avatar
  • 192
1 vote
0 answers
147 views

How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
Soerendip's user avatar
  • 1,295
5 votes
0 answers
30 views

Iupred definition of long/short form disorder

I need to predict disorder of proteins and here there is a description of Iupred in its two variants, long and short-disorder. This is a manuscript defining the method. I couldn't find a precise ...
aerijman's user avatar
  • 645
4 votes
2 answers
735 views

Plotting coverage of annotation over collection of region

I'm trying to plot "meta" coverage of annotation: i.e. features (eg. gene class) over certain regions. It is similar to read coverage plots over gene body, except my input is two bed files (both in ...
Siddharth's user avatar
  • 345
5 votes
2 answers
836 views

full visualisation of draft genomes alignment

I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (genome1.fasta) and one with ~1'000 contigs (...
aechchiki's user avatar
  • 2,676
0 votes
1 answer
447 views

Exporting nt's differences from MEGA alignment

I have an alignment of some full genome sequences of DENV1 that we have recently sequenced from the serum of patients. I have already cleaned the sequences, built the alignments and done the SNPs ...
Fabiana's user avatar
1 vote
0 answers
145 views

Colinearity analysis with respect to gene orientation

I was reading the manual of MCScanX and found that besides a all-vs-all protein blast file the tool takes a gtf file with four columns only: scaffold name, protein name, from, to. As the tool is not ...
Kamil S Jaron's user avatar
4 votes
1 answer
741 views

How to map short sequences to long reads, recovering all multiply-mapped high-quality matches

The dilemma: I have around one million short sequences (21 bp to several 100s of basepairs) for which I need to identify all occurrences of in 20-30x coverage noisy long reads (both pacbio and ONT). ...
conchoecia's user avatar
  • 3,141
1 vote
0 answers
55 views

case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
aure_bobo's user avatar
9 votes
1 answer
131 views

Best practices for deciding if two structural variants are actually the same variant?

I know that I can use bcftools isec to compare two VCF files containing single nucleotide variants (SNVs); it will generate four possible output files: one with all ...
mdperry's user avatar
  • 258
6 votes
2 answers
144 views

Deciding which samples go in which batch

I have 370 samples to sequence, we probably will end up using only 96 samples per run (due to the barcode with the primers we'll use). This means running 4 batches. To minimize the batch effect I need ...
llrs's user avatar
  • 4,693
8 votes
2 answers
2k views

estimate genome size: kmer-based approach from PacBio reads

Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)? Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
aechchiki's user avatar
  • 2,676
1 vote
0 answers
101 views

Detect gene duplication events from a whole genome in FASTA format

Are there any tools for finding duplications from a whole genome in FASTA format? Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the ...
Biomagician's user avatar
  • 2,459
1 vote
0 answers
38 views

Which secondary structure prediction algorithms don't query the PDB/DSSP for known homologous sequences?

There are several secondary structure prediction algorithms. I am interested in the algorithms which predict secondary structure without accessing the PDB to cheat by using the DSSP or STRIDE entry ...
Aalawlx's user avatar
  • 517
4 votes
2 answers
90 views

Do any computational phylogenetic methods enable the specification of ancestral states?

Various phylogenetic algorithms estimate ancestral states of a phylogenetic dataset. Is there a way in either maximum parsimony, distance-based methods, or Bayesian inference to indicate what the ...
Namenlos's user avatar
  • 317
0 votes
2 answers
97 views

Why does `pratchet()` in `phangorn` not find the most parsimonious trees?

I called pratchet() on a dataset with binary values for the characters and it returned a parsimony value of 35. I then calculated the parsimony value for the ...
Namenlos's user avatar
  • 317
1 vote
0 answers
22 views

XCMS isn't evaluating the proper peak due to retention time drift

I'd like to do a targeted screening analysis for trace contaminates. However, due to the nature of the sample preparations, the retention times I'm getting drift a lot from run to run and XCMS isn't ...
virtualxtc's user avatar
7 votes
3 answers
2k views

visualisation of genome alignment

I was asked to check the synteny of some genes in two genome assemblies of the same species (PacBio & Illumina). I was given two scaffolds couples (so 4 scaffolds total) in the Illumina genome and ...
aechchiki's user avatar
  • 2,676
6 votes
1 answer
105 views

How to efficiently compute the exact percentage of non-unique k-mers in a genome for given k?

I'm looking for some software that can "efficiently" (time and memory) compute the exact percentage of non-unique k-mers in a genome for given k. I don't need the k-mers or the abundances itself, I ...
Jens's user avatar
  • 69
3 votes
1 answer
891 views

gffread: GFaSeqGet errors on coordinate overhang

Disclaimer: I had this issue posted on Tuxedo Tools users group and shared it on Twitter, but could not get an answer to this from the developers, nor find documentation of this issue online. So, I'll ...
aechchiki's user avatar
  • 2,676
4 votes
2 answers
289 views

Exon-exon junctions: compare experimental transcripts to reference annotation

My aim is to parse an experimental transcript set (obtained by RNAseq) to check which splice junctions are already reported in a reference annotation and which ones are new. I tried ...
aechchiki's user avatar
  • 2,676
2 votes
2 answers
1k views

What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve?

What software/tool can I use to visualise a multiple sequence alignment in the xmfa format as produced by command-line tool Mauve? I am particularly interested in seeing the single nucleotide ...
Biomagician's user avatar
  • 2,459