Can you recommend a DNA alignment program that can sort heterogeneous sequences into groups and produce multiple consensuses?
For example
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Aligning heterogeneous DNA sequences into multiple consensuses
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Automating consensus sequence generation...?
I have a rather straightforward problem. I'm doing a pop. gen. study which has ~1200 individuals. Using our Miseq, I've generated short (~150b) fragments... -
localized consensus build instead of scaffolding
I am trying to make something out of a denovo, heterozygous plant WGS.
it won't go past a contig stage (scaffolding improved average contig length... -
multisample variant calling and consensus sequences
Hi,
I have used BWA to map reads from ~45 individuals of my favorite species to a reference (haploid) mitochondrial DNA sequence. My goal... -
consensus sequence with samtools and bcftools 1.2
Hi,
I want to build a consensus sequence for a small region of the genome from an individual in 1000genomes. Here's what I did:
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Is it possible to create a consensus sequence from a fasta file?
Hello,
The fasta file includes DNA sequences of a target region generated from a pooled sample, is there any way to create a consensus... -
Is it possible to create a consensus sequence from a fasta file?
Hello,
The fasta file includes DNA sequences of a target region generated from a pooled sample, is there any way to create a consensus sequence...Last edited by ssnowfox; 02-12-2015, 12:50 PM. -
How to handle heterozygous INDELS
Hey,
how do you handle INDELS which show in a .vcf file a heterozygous status. Meaning there are two alleles in the sample: 50% of the... -
Consensus sequence out of BAM+VCF with low coverage areas masked?
Hello!
I'm wondering if it's possible to create a consensus sequence that combines the data of BAM/SAM files and filtered VCF files so... -
Getting the consensus file from a reference based alignment
Hi,
I have a Mapped genome fasta file with chromosomes scaffolds and a denovo contigs sequences all together in a Multifasta file.
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building consensus with multiple samples
Hi,
I have 4 samples with Illumina reads which I would like to build a consensus out of. The 4 samples are of the same species and there... -
vcfutils to get consensus sequence
There have been several posts about this, but it has been a while, and my queries are not completely answered, so thought I would put it down again.... -
samtools -> fasta
Hello, Thanks in advance for any help!
I have RNAseq data from a dozen or so individuals assembled to a reference transcriptome using CLC and wish... -
Problem calling consensus sequence with Samtools mpileup?
Hi all, I hope someone can help, have you come across anything like this yourself? I have several bacterial strain BWA genome assemblies.... -
Why are there all these As in my consensus sequence: An issue with samtools pileup
Hey folks,
I've run into an interesting problem. I've aligned a bunch of 454 reads from one species against the reference genome of a...
