BOL

Hmmm great link Rahul, You can also try Mugsy: fast multiple alignment of closely related whole genomes http://bioinformatics.oxfordjournals.org/content/27/3/334

In my works, I have also used BWA-SW, BLAT and LASTZ. However, LASTZ is not well-suited for aligning to many chromosomes at once. Whereas, the BLAT is difficult as PSL to BAM conversion is imperfect in it.

Thanks for the useful list.

I found this CUTADAPT useful. It searches for the adapter in all reads and removes it when it finds it.http://cutadapt.readthedocs.org/en/stable/guide.html

Broad Institute listed many new tools for genome assembly, please all at http://www.broadinstitute.org/scientific-community/software?criteria=Assembly

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

MaGuS (Map-GUided Scaffolding) is a scaffolder and a reference-free evaluator of assembly quality. It uses a draft genome assembly, a genome map, and high-throughput sequencing paired-end data. It has been succesfully tested on the Arabidopsis genome with Illumina reads and a Whole-Genome Profiling (WGP) map.

https://github.com/institut-de-genomique/MaGuS