All Questions
Tagged with assembly sequence-alignment
13
questions
1
vote
0
answers
149
views
bwa mem hangs after a few thousand reads
I am trying to align a bunch of paired sample fastq files using bwa mem.
My original command was:
...
- 19
2
votes
1
answer
82
views
What is the best way to process yeast genomes?
I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis.
I have a reference genome (S288C) to use for ...
- 1,033
0
votes
1
answer
218
views
Why must a maximal non-branching path be a contig?
The following is from Bioinformatics Algorithms:
Fortunately, we can derive contigs from the de Bruijn graph. A path in a graph is called non-branching if in(v) = out(v) = 1 for each intermediate ...
- 127
1
vote
1
answer
565
views
where to find sample contig data
Where or How can I find contigs? I am trying to learn Bioinformatics and I want to make a reference-based gene search. I also want to align contigs with a given reference sequence. From NCBI other ...
- 73
4
votes
1
answer
834
views
Difference between genome assembly and genome sequence alignment to a reference to find structural variants
I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations.
I've been ...
- 41
2
votes
1
answer
260
views
What is the meaning of these misaligned reads in a sequencing run?
I am analyzing some SARS-CoV-2 sequencing runs abd often find read alignments like the one in the image.
...
- 359
2
votes
0
answers
353
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 ...
- 21
1
vote
4
answers
915
views
Tools for comparing/visualizing FASTAs?
I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this.
What tools/methods exist to compare two FASTAs and see the difference in ...
- 1,423
1
vote
1
answer
38
views
Finding simple sequence from reads with significant overlap
I wrote a "script" to pull out reads from a huge fastq file in an iterative manner, by finding homology to the previous sequence.
It should be relatively easy to overlap them and assemble ...
- 113
6
votes
1
answer
132
views
Is there a way to assemble contigs starting from a specific sequence?
My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
- 1,007
5
votes
3
answers
5k
views
How to get fasta alignment file from SAM/BAM file?
I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's ...
- 367
9
votes
2
answers
2k
views
Is there a standard definition for "assembly polishing"?
Is there a standard definition for "assembly polishing" in the field?
Is there a standard definition for what polishing algorithms do?
My understanding of "polishing" is strongly influenced by ...
- 1,423
4
votes
2
answers
439
views
Reordering scaffolds according to a reference without a genetic map
I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
- 325