WEAV still needs to be stable. If any of you find bugs, please let us know the situation. It will be very helpful for us to fix it. Please check Bugs and Errors .

• Introduction
• WEAV
• WEAV-CLUSTERING
• Test
• Bugs and Errors
• Authors

Introduction

WEAV wants to be general sequence assembler including genomic sequence assembler, whole transcriptome assembler, metagenomic sequence assembler, and so on. However, we only tested transcriptome assembly, and will test the other cases.

• de novo whole transcriptome assembly: You may need to cluster the read set first (but not necessarily). Therefore, you need to use WEAV-CLUSTERING first and then use WEAV to assemble clusters prepared by WEAV-CLUSTERING.
• de novo assembly (general assembly): You just use WEAV as an assembler like Velvet, ABySS and so on.

WEAV

A de novo whole transcriptome assembler which can simultaneously assemble multiple isoforms for a or more genes together. We have not yet tested genome assembly, but we believe that ours can work for it.

Downloads: Find the latest tar ball with weav_ header.

Compilation Guide

General Manual (contig.in)

WEAV-CLUSTERING

A read set may be composed by many genes and each gene may have more than one isoforms. In this case, reconstruct all the transcripts by one shot would be extremely difficult or impossible. Therefore, dividing the read set into several smaller read set, called WEAV-CLUSTERING, would be helpful. Moreover, if we can make a read set has only one gene or few genes, it can be a crucial step. Here we introduce a tool to cluster the read set.

Downloads: Find the latest tar ball with weav-clustering_ header.

Manual for WEAV-CLUSTERING : This includes how to download, compile and run.

Test

You can test the performance of WEAV by test read set (see Test Wiki). There you can find uniqueness of WEAV, and you can compare it with the other assemblers using same test read set.

Test Wiki

Bugs and Errors

WEAV is not stabilized yet. We promise that we will do our best to fix bugs and errors you would meet. Please let us know what kind of problem you've met. We will be very happy to see whatever information about the problem. Please check the following Wiki and please help us by providing the information.

Bugs and Errors

Authors