modified: INSTALL.sh

	modified:   README.md
	modified:   assemblatron.py

Author: J35P312

INSTALL.sh

@@ -8,3 +8,9 @@ pip install BESST
 
 cd scripts
 python setup.py build_ext --inplace
+
+cd ..
+
+git clone https://github.com/ablab/quast.git
+cd quast
+pip install -e .

README.md

@@ -15,7 +15,7 @@ The full workflow involves:
 
     3: alignment of the contigs
 
-    4: compute assembly statistics
+    4: Quality control, using assemblatron stats or quast
 
     5: variant calling
 
@@ -26,10 +26,9 @@ The assemblatron workflow is run through the following commands:
 
 run the install script:
 ./INSTALL.sh
-The install script will download and install BESST, fermikit, and tiddit.
+The install script will download and install BESST, fermikit, and quast.
 Dependencies:
 
-	vcftools
 	samtools
 	python 2.7
 	bwa
@@ -71,12 +70,23 @@ Assemblatron performs alignment using bwa mem. The output is printed to a file n
 A bam file named <prefix>.bam will be produced
 
 # Stats
-compute various statistics of an assembly. THe output is printed to stdout.
+compute various statistics of an assembly. The output is printed to stdout.
 
-python assemblatron.py --stats <contigs_bam>
+python assemblatron.py --stats --bam <contigs_bam>
 
 The statistics include N50, L50, assembly size, and the number of contigs.
 
+# Quast
+
+The quality control may be  performed using quast. Quast performs a more in-depth but slower analysis.
+
+python assemblatron.py --quast --fasta <contigs_fasta> --output <output_folder>
+
+python assemblatron.py --quast --fasta <contigs_fasta> --ref <reference.fasta> --output <output_folder>
+
+The statistics module supports any number of fasta files. Type --help for more information. 
+NOTE: use absolute path for the output directory.
+
 # SV
 Call SV. Assemblatron will calssify variants as DEL, INV, BND (translocation or complex), INS, and TDUP.
 
@@ -102,7 +112,7 @@ Call indels and SNV using htsbox pileup (same as fermikit).
 
 the  output is printed to stdout
 
-other options:
+options:
 
   -h, --help  show this help message and exit
   --bam BAM   input bam (contigs)
@@ -140,3 +150,7 @@ Cite the components that you used, as well as the Assemblatron git hub page.
 	If you performed scaffolding, please cite the BESST paper:
 
 		https://github.com/ksahlin/BESST
+
+	For more info on QUAST:
+
+		https://github.com/ablab/quast

assemblatron.py

@@ -35,6 +35,7 @@ def assemble(args,wd):
 parser.add_argument('--align'          , help="align contigs to reference using bwa mem", required=False, action="store_true")
 parser.add_argument('--fasta'      , help="convert aligned contigs bam file to fasta", required=False, action="store_true")
 parser.add_argument('--fastq'      , help="convert bam to fastq", required=False, action="store_true")
+parser.add_argument('--quast'        , help="compute assembly stats using quast", required=False, action="store_true")
 
 args, unknown = parser.parse_known_args()
 
@@ -79,6 +80,25 @@ def assemble(args,wd):
 	args= parser.parse_args()
 
 	stats.assembly_stats(args)
+elif args.quast:
+
+        parser = argparse.ArgumentParser("""QUAST - quality control""")
+        parser.add_argument('--quast'        , help="compute assembly stats using quast", required=False, action="store_true")
+        parser.add_argument('--contigs', nargs='*', help="input contigs (multiple assemblies are allowed)", required=True)
+        parser.add_argument('--ref',required = False,type=str, help="reference fasta")
+        parser.add_argument('--output',required = True,type=str, help="output folder")
+	parser.add_argument('--features',nargs='*',required = False,type=str, help="Feature BED/GFF file")
+        parser.add_argument('--len',default=100,type=int, help="minimum contig length (default= 100 bp)")
+        args= parser.parse_args()
+
+	quast="quast.py {} --output-dir {} --min-contig {}".format(" ".join(args.contigs),args.output,args.len)
+
+	if args.ref:
+		quast+=" -r {}".format(args.ref)
+
+	if args.features:
+		quast+=" -g {}".format(" ".join(args.features))
+	os.system(quast)
 
 elif args.align:
 	parser = argparse.ArgumentParser("""Assemblatron align - align contigs to the reference using bwa mem""")
@@ -115,6 +135,8 @@ def assemble(args,wd):
 	parser.add_argument('--mem'      , help="maximum  mempry per thread (gigabytes)", type=int, default=4)
         parser.add_argument('--iter'      , help="Number of itterations (default = 500000)", type=int, default=500000)
 	parser.add_argument('--cores'       ,type=int, default = 8, help="number of cores (default = 2)", required=False)
+        parser.add_argument('-q'       ,type=int, help="minimum mapping quality for scaffolding", required=False)
+        parser.add_argument('-p'       ,type=int, help="minimum number of read-pairs to create edge", required=False)
 	args= parser.parse_args()
 
 	args.prefix=args.filename
@@ -132,10 +154,17 @@ def assemble(args,wd):
 	os.system("samtools index {}".format(args.bam))
 
 	if args.rf:
-		os.system("runBESST -c {} -f {} -orientation rf -o {} --iter {}".format(args.contigs,args.bam,args.output,args.iter))
+		besst="runBESST -c {} -f {} -orientation rf -o {} -plots --iter {}".format(args.contigs,args.bam,args.output,args.iter)
 	else:
-		os.system("runBESST -c {} -f {} -orientation fr -o {} --iter {}".format(args.contigs,args.bam,args.output,args.iter))
-	
+		besst="runBESST -c {} -f {} -orientation fr -o {} -plots --iter {}".format(args.contigs,args.bam,args.output,args.iter)
+
+	if args.q:
+		besst+= " --min_mapq {}".format(args.q)
+
+	if args.p:
+                besst+= " -e {}".format(args.p)
+
+	os.system(besst)
 elif args.fastq:
 
 	parser = argparse.ArgumentParser("""Assemblatron fastq - converts bam to fastq using samtools""")