I noticed that information on SNP calling and SNP discovery (especially!) software for NGS is quite scarce. Are there any good tools available from non-commercial sources? Could you suggest any titles (and corresponding URLs) one would want to look at? I am specifically looking for solutions for a robust secondary data analysis pipeline in a non-profit environment, for the data from virtually all platforms/read lengths, including 454, Illumina, SOLiD, and future platforms suich as PacBio, Ion Torrent, etc. Maybe we could start a list of such software here, with some details on which software is best for what kind of data. Thanks!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
I've found MAQ to be very good tool for SNP calling, but I'm not sure if it can handle larger reads. I use it with Illumina data.
-
-
Gatk
Check out the genome analysis tool kit (GATK) developed at the Broad:
The UnifiedGenotyper is one of the task this toolkit has, but there are plenty of other great tools there. Good luck!
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
Yesterday, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
58 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
45 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
55 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment