benjamindn/evar repository overview

reference genome in .fa 
genomic annotation in .gff
single-end one file fastq.gz or double-end two files R1.fastq.gz R2.fastq.gz

! your reference can't have any N in place of A, T, G or C --> sript will crash

# -r = remove-adapter-fwd (str)
# -c = remove-adapter-rev (str)
SGA_PREPROC_FLAGS:= -r AGATCGGAAGAGCACACGTCTGAACTCCAGTC -c AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG

# -x = min x kmer coverage in a read (int)
# -k = size of kmer (int)
SGA_FILTER_FLAGS:= -x15 -k61

# -m = minimum overlap required between two reads to merge (int)
SGA_FMMERGE_FLAGS:= -m61

# -k = size of kmer (int)
SGA_KMERCOUNT_FLAGS:= -k61

# -t = number of thread (int)
SGA_THREAD:= -t4

# -m = minimum overlap required between two reads to merge (int)
SGA_OVERLAP_FLAGS:= -m61

REF = ref.fa
REF_GFF = ref.gff

SGA_PREPROC_FLAGS:= -r AGATCGGAAGAGCACACGTCTGAACTCCAGTC -c AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG
SGA_FILTER_FLAGS:= -x15 -k61
SGA_FMMERGE_FLAGS:= -m61
SGA_KMERCOUNT_FLAGS:= -k61
SGA_THREAD:= -t4
SGA_OVERLAP_FLAGS:= -m61

Some parameters of rules were not in parameters but can be change in the original makefile
For more details on parameters see the help for SGA, BWA and samtools

```
docker run --rm -v $(pwd):/export benjamindn/evar-call fastq.all
```

#all your reads are mapped
.bwamem.bam

#De novo assembly 
.preproc.filter.pass.kmercount.bwamem.bam

#Region of interest by kmer
.preproc.filter.pass.rmdup.merged.bwamem.bam

The best way to visualize your result is to put together the de novo assembly and the region of interest in IGV

Create a directory data 
Put your fastq.gz, reference.fa and annotation.gff in this directory
Go in the data directory
Run this command 
```
docker run --rm -v $(pwd):/export benjamindn/evar-call fastq.all
```
Wait for all the processus (more your genome to analyse is big more times is needed)
At the end you get the three files for an IGV visualisation, a file in .tsv you can open with a tablesoftware, a repartition plot of mutation and an interactive assembly network to see the de novo assembly.  

work in progress