I have 53 samples which belongs to two treatments. In each sample, I started with 2X100 Illumina metagenomic data and have used SOAPdenovo2 to generated contigs. I want to combine all contigs (>10000bp) from all samples and align all contigs. I want to have alignment map or contigs map. Final goal is to find contigs which are unique to each treatment. I have no idea how to do it? Could anybody help me?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
One of my programs, Dedupe (packaged together with BBMap), is designed to find duplicate and unique contigs. You can run it like this:
dedupe.sh in=assembly1.fa,assembly2.fa,assembly3.fa out=unique.fa uniqueonly=t
Optionally, you can allow some mismatches, edits, or set various other constraints.
That will output all of the unique stuff and throw away anything with any duplicates. You should first rename the contigs so you know which assembly they came from. If you only have 2 treatments, I would suggest first merging all of the reads from a treatment and assembling them together so you only have 2 assemblies (if I correctly understand your problem).
-
Comment
-
Hmmm... other than dedupe, I don't really have any relevant tools. I'm not sure how to best go about that; you might need to write something yourself.
As for dedupe, you could process all the assemblies together, allow some edit distance, set "uniqueonly=t", and set the "outd" flag to save all of the duplicate contigs. For example:
dedupe.sh in=assembly1.fa,assembly2.fa,assembly3.fa outd=duplicate.fa uniqueonly=t e=10
The run dedupe again on the duplicates:
dedupe.sh in=duplicate.fa out=core.fa e=10
This is not a perfect solution, but it will give you a file with exactly one copy each of all the contigs that appear at least twice in the input.
-Brian
Comment
Latest Articles
Collapse
-
by seqadmin
Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.
Nucleic Acid Quality Control
Preparing for NGS starts with isolating the...-
Channel: Articles
02-10-2025, 01:58 PM -
-
by seqadmin
In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...-
Channel: Articles
01-27-2025, 07:46 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Genetic Mapping of Plasmodium knowlesi Identifies Essential Genes and Drug Resistance Mechanisms
by seqadmin
Started by seqadmin, 02-07-2025, 09:30 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
02-07-2025, 09:30 AM
|
||
Started by seqadmin, 02-05-2025, 10:34 AM
|
0 responses
104 views
0 likes
|
Last Post
by seqadmin
02-05-2025, 10:34 AM
|
||
Started by seqadmin, 02-03-2025, 09:07 AM
|
0 responses
83 views
0 likes
|
Last Post
by seqadmin
02-03-2025, 09:07 AM
|
||
Started by seqadmin, 01-31-2025, 08:31 AM
|
0 responses
45 views
0 likes
|
Last Post
by seqadmin
01-31-2025, 08:31 AM
|
Comment