I am looking for free sequence assembly software for Mac. Until now I have worked on Windows but now I have to work in Macbook. Please suggest some free software to me.
It will depends of the sequence type that you want to assembly (transcriptome vs genome; Sanger vs NGS).
+ For standard Sanger sequence assemblies, you can use the old Phrap that is free of charge for academics licences (http://www.phrap.com/priceinfo.htm). Other option is CAP3 (http://seq.cs.iastate.edu/cap3.html). You also can use CAP3 via web (http://pbil.univ-lyon1.fr/cap3.php)
+ For NGS (genomes), Illumina for example, you can use ABySS (http://www.bcgsc.ca/platform/bioinfo/software/abyss)(You can download a precompiled version). Other assemblers such as ALLPATH-LG or SOAPdenovo should be compiled in the system before use them, and I am not sure if they will work. There is also a version of the WGS assembler (CABOG) for OSX (http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-7.0/). Keep in mind that assembly a genome bigger than a bacteria using Illumina require high coverage and a system with a lot of RAM memory (up to 128 Gb).
+ If you want to assembly transcriptomic data, Trinity may be a good tool to consider (http://trinityrnaseq.sourceforge.net/) but again, probably you will need a lot of RAM.
If you need to compile any of these tools you will need to install Xcode (https://developer.apple.com/xcode/) and the Command Line Tools for Xcode (http://www.mkyong.com/mac/how-to-install-gcc-compiler-on-mac-os-x/)
Good luck !!!
It will depends of the sequence type that you want to assembly (transcriptome vs genome; Sanger vs NGS).
+ For standard Sanger sequence assemblies, you can use the old Phrap that is free of charge for academics licences (http://www.phrap.com/priceinfo.htm). Other option is CAP3 (http://seq.cs.iastate.edu/cap3.html). You also can use CAP3 via web (http://pbil.univ-lyon1.fr/cap3.php)
+ For NGS (genomes), Illumina for example, you can use ABySS (http://www.bcgsc.ca/platform/bioinfo/software/abyss)(You can download a precompiled version). Other assemblers such as ALLPATH-LG or SOAPdenovo should be compiled in the system before use them, and I am not sure if they will work. There is also a version of the WGS assembler (CABOG) for OSX (http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-7.0/). Keep in mind that assembly a genome bigger than a bacteria using Illumina require high coverage and a system with a lot of RAM memory (up to 128 Gb).
+ If you want to assembly transcriptomic data, Trinity may be a good tool to consider (http://trinityrnaseq.sourceforge.net/) but again, probably you will need a lot of RAM.
If you need to compile any of these tools you will need to install Xcode (https://developer.apple.com/xcode/) and the Command Line Tools for Xcode (http://www.mkyong.com/mac/how-to-install-gcc-compiler-on-mac-os-x/)
Good luck !!!
thanks a lot Aureliano. I will assemble standard sanger sequence. Let me try you suggestions.
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