Does anybody know an opensource software package for whole genome assembly of cDNA with Illumina paired-end sequencing? I'm really looking for an assembler designed for cDNA data, not DNA. I don't think that programs like Velvet or SSAKE can deal with this kind of data (I may be wrong). MIRA seems OK but it is not quite clear whether it takes the "paired-end" feature into account when assembling cDNA data. Any help is much appreciated !!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
-
Thx Zigster. Yes I mean the transcriptome assembly. After some research, it seems that MIRA can deal with this kind of data (EST + paired end + short read). I saw in several papers that CAP3 was used on the assembled contigs (to get larger contigs). Is this a good idea ? Do you have any advice ?
Comment
-
if you have 100M short reads I would give those to Velvet and then use those contigs in an alignment based program like you mentioned
i like Mira but the parameter setup is a hassle. Prepare to set aside a couple hours to read the manual.
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
72 views
0 likes
|
Last Post
by seqadmin
02-07-2025, 09:30 AM
|
||
Started by seqadmin, 02-05-2025, 10:34 AM
|
0 responses
113 views
0 likes
|
Last Post
by seqadmin
02-05-2025, 10:34 AM
|
||
Started by seqadmin, 02-03-2025, 09:07 AM
|
0 responses
90 views
0 likes
|
Last Post
by seqadmin
02-03-2025, 09:07 AM
|
||
Started by seqadmin, 01-31-2025, 08:31 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
01-31-2025, 08:31 AM
|
Comment