Reference genome database for Bowtie2
======

Bowtie2 is a classical ultrafast short sequence aligner.

 - Website: http://bowtie-bio.sourceforge.net/bowtie2/
 - Citation: Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2.
   Nature Methods. 2012. 9(4):357-359.

Built using Bowtie2 v2.4.5. Command:

```
bowtie2-build --seed 42 --threads # db.fna WoLr2
```

Compatible with: Bowtie2 v2.x

Basic search commands:

```
# single FASTA file:
bowtie2 -p # -x WoLr2 -f input.fa -S output.sam
# unpaired FASTQ file:
bowtie2 -p # -x WoLr2 -U input.fq -S output.sam
# paired-end FASTQ file:
bowtie2 -p # -x WoLr2 -1 input.R1.fq -2 input.R2.fq -S output.sam
```

Search with high sensitivity (recommended for metagenomics):

```
bowtie2 -p # -x WoLr2 -1 input.R1.fq -2 input.R2.fq -S output.sam \
  --very-sensitive
```

Minimize output alignment file size (no header, no unaligned, no alignment
sequences and scores, compress SAM file):

```
bowtie2 -p # -x WoLr2 -1 input.R1.fq -2 input.R2.fq --very-sensitive \
  --no-head --no-unal | cut -f1-9 | sed 's/$/\t*\t*/' | gzip > output.sam.gz
```

SHOGUN-default search command (optimized for shotgun metagenomics):

```
bowtie2 -p # -x WoLr2 -f input.fa -S output.sam --seed 42 \
  --very-sensitive -k 16 --np 1 --mp "1,1" --rdg "0,1" --rfg "0,1" \
  --score-min "L,0,-0.05" --no-head --no-unal
```

Output file format: SAM

This analysis requires at least 68 GB memory.