<p>Dear lazyweb,</p>

<p>my question is somehow related to some previous questions asked here: ( <a href='http://biostar.stackexchange.com/questions/788'>http://biostar.stackexchange.com/questions/788</a> , <a href='http://biostar.stackexchange.com/questions/31'>http://biostar.stackexchange.com/questions/31</a>, <a href='http://biostar.stackexchange.com/questions/613'>http://biostar.stackexchange.com/questions/613</a> , etc...).</p>

<p>I'm looking for a table that would summarize the pro's and the con's of each tool for NGS (mappers and/or snp callers), the algorithm used, if the quality of the fastq, is taken into account,  how the gaps &amp; the indels are handled, a publication, etc...
... e.g.: something that would look like the following  (almost empty) page on wikipedia: <a href='http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment'>http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment</a></p>

<p>Thanks, </p>

<p>Pierre</p>

<p><strong>UPDATE:</strong> <a href='http://twitter.com/#!/Julien_f'>@Julien_f</a> suggested this link: <a href='http://lh3lh3.users.sourceforge.net/NGSalign.shtml'>http://lh3lh3.users.sourceforge.net/NGSalign.shtml</a></p>

<p><strong>Update2</strong>: another cool resource cited in Marc's paper: <a href='http://seqanswers.com/wiki/Software/list'>http://seqanswers.com/wiki/Software/list</a></p>

<p>Although there are over 30 aligners, I guess 90% of researchers only choose from the list below:</p>
<ul>
<li>Illumina: Bowtie, BWA, Mosaik and Novoalign (Stampy is also a good one)</li>
<li>SOLiD: Bfast, Bowtie and BWA (perhaps also NovoalignCS?)</li>
<li>454: SSAHA2, LAST, BLAT and Mosaik (I would recommend BWA-SW actually)</li>
</ul>
<p>Carefully studying their features would not take much time. In addition, to "feel" a tool, we'd better use it rather than just look at the feature table.</p>
<p>As to SNP callers, I guess 90% who do not write in-house tools are using GATK and SAMtools/MAQ. SNVMix is also a good one, especially for cancer sequencing. As there are only a few of them, it is easy to try each.</p>
<p>In addition, usual SNP calling on deep resequencing data is not hard. Many groups use their in-house tools and being highly tuned for specific data, in-house tools may have better performance.</p>
<p>At last, as I am promoting everywhere, apply BAQ implemented in samtools. Doing this will improve the accuracy for all SNP callers so far.</p>