assemblet
=========

Short read assembler for assembling antigenic variant sequences
in bacteria.

The input should be high-throughput sequencing reads of DNA obtained
by PCR amplification of a small region (several kilobases) that is
believed to undergo antigenic variation.

Requirements:

- Python 2, version 2.6 or higher
  (some components work much faster in PyPy)

- nesoni
  http://www.vicbioinformatics.com/software.nesoni.shtml

- matplotlib 
  (only needed for some tools)


Example usage
=============

mkdir output



nesoni clip: output/negative --match 1 --length 50 pairs: data/negative_R?.fastq.gz

pypy assemblet.py new: output/negative --k 50

pypy assemblet.py load: output/negative \
    interleaved: output/negative_paired.fq.gz \
    reads: output/negative_single.fq.gz



nesoni clip: output/positive --match 1 --length 50 pairs: data/positive_R?.fastq.gz

pypy assemblet.py new: output/positive --k 50

pypy assemblet.py load: output/positive \
    interleaved: output/positive_paired.fq.gz \
    reads: output/positive_single.fq.gz



pypy assemblet.py assemble: output/assembly \
    samples: output/negative output/positive

pypy assemblet.py select: output/selection output/assembly.fa data/reference.fa \
    samples: output/negative output/positive

python assemblet.py validate: output/validation output/selection.fa \
    samples: output/negative output/positive

python assemblet.py quantify: output/quantification output/selection.fa \
    samples: output/negative output/positive



# If you have zero interest in SNPs:

pypy assemblet.py assemble: --skip-snps yes \
    output/assembly-nosnp \
    samples: output/negative output/positive

pypy assemblet.py select: --snp-weight 0.0 \
    output/selection-nosnp output/assembly-nosnp.fa data/reference.fa \
    samples: output/negative output/positive