ohnosequences/metapasta — pull request #35 by eparejatobes (2014-05-22 16:22:14+00:00)
Title: current state of metapasta

### input
* **samples**: name, left FAST/FASTQ, right FAST/FASTQ (can be the same)
* **index for 16S database** in BLAST of LAST format (Era7 nt.16s database is included)
* **configuration**: email, name, command line for LAST/BLAST

### output
* logs of LAST/BLAST
* **csv tables** with columns: `tax_id`, `rank`, `name`, for each sample: `count`, `acc_count`, `total`
* taxonomy tree with assignment in pdf
* (optional) dynamodb table with `hash`, `read_id`, `tax_id`, `seq`, `quality`
* (optional) dynamodb table with `sample`, `hash`

### pipeline
* FLASH merge
* BLAST/LAST mapping, choosing best hit for every read
* *reduce*: generation tables

### unimplemented
* the *lowest common ancestor* paradigm
*output in BAM format??