# Design of the FASTQ Geno2Pheno Step #
## Using Gotoh mapping ##
Until version 7.6, this was the sam_g2p step, because we first mapped the reads
with bowtie2, then applied the G2P algorithm to bowtie2's SAM output. Some of
the V3LOOP samples mapped very badly to the HIV references, so we decided to try
using Gotoh pairwise mapping, as described in issue #370. We chose the
HIV1-C-BR-JX140663-seed reference to align against, because that's the one that
most closely aligns to the reference used in our G2P library.

## Minimum Gotoh alignment score ##
In issue #395, we found that samples with no HIV in them were still mapping
some reads to V3LOOP, sometimes thousands of reads. When we plotted the
alignment scores, it was clear that our minimum score was too low.

![Alignment scores](images/v3loop_alignment_scores.png)

We changed the minimum score to be halfway between the two clusters of scores.
# Design of the FASTQ Geno2Pheno Step #
## Using Gotoh mapping ##
Until version 7.6, this was the sam_g2p step, because we first mapped the reads
with bowtie2, then applied the G2P algorithm to bowtie2's SAM output. Some of
the V3LOOP samples mapped very badly to the HIV references, so we decided to try
using Gotoh pairwise mapping, as described in issue #370. We chose the
HIV1-C-BR-JX140663-seed reference to align against, because that's the one that
most closely aligns to the reference used in our G2P library.

## Minimum Gotoh alignment score ##
In issue #395, we found that samples with no HIV in them were still mapping
some reads to V3LOOP, sometimes thousands of reads. When we plotted the
alignment scores, it was clear that our minimum score was too low.

![Alignment scores](../images/v3loop_alignment_scores.png)

We changed the minimum score to be halfway between the two clusters of scores.
Fix path to alignment scores plot.
Fix path to alignment scores plot.
