De Novo Transcriptome Assemblers – Oases, Trinity, etc.
We are working on an article on de novo transcriptome assemblers, and it will be released in following four parts this week. Stay tuned !! Part 1 – Larger Perspective Part 2 – Trinity and Oases – Quick...
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De Novo Transcriptome Assemblers – Oases, Trinity, etc. – II
We present our apologies for not writing for a while, dear reader. By now you realize that thinking and creativity do not come to us naturally, or otherwise we would be writing fictions or peddle...
View ArticleDe Novo Transcriptome Assemblers – Oases, Trinity, etc. – III
Oases and Trinity – Quick Start Guide This guide is for those, who like to get started quickly with available transcriptome assemblers. So far, our experiences had been with Oases and Trinity only. If...
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De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV
Assembly Algorithms of Trinity (and Oases) We did not find much information on Oases algorithm in public domain except this small note at the Oases website - Oases uploads a preliminary assembly...
View ArticleTrinity and Contrail for Color Space
We do not know how many of you work on ABI-SOLiD data. We modified the codes of Trinity transcriptome assembler and Contrail genome assembler for color space, and are in the process of testing them. If...
View ArticleUpdating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps
The entire process should take about an hour or so depending on how long you spend on the last step. Step 1. Go to your local supermarket and bring a bottle of good wine [estimated time - 20 minutes]....
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Explaining Output of Trinity Component – Inchworm
The transcriptome assembler Trinity from Broad Institute runs through three steps – Inchworm, Chrysalis and Butterfly. Inchworm is the first program of the pipeline. It operates on the RNAseq library...
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Can Trinity be Used for Genome Assembly?
For new readers, easiest way to follow us is through our twitter feed. The feed is updated, whenever we post a commentary here. A reader asked by private email whether Trinity can be used for genome...
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