Skip to main content
. Author manuscript; available in PMC: 2018 Jan 24.
Published in final edited form as: J Comput Biol. 2017 Apr 18;24(11):1071–1080. doi: 10.1089/cmb.2017.0013

Table 2.

Software Used in the U50 Package

Program/language Version Application Execution order
Bowtie2 2.2.4 Maps contigs to reference, creating an SAM file
(Langmead and Salzberg 2012)		 1
SAMtools 1.2 Converts SAM to BAM (Li 2011; Li et al. 2009) 2
BEDTools 2.17.0 Converts BAM to BED (Quinlan and Hall 2010) 3
Python
(BioPython) 		2.7.3
1.66		 Executes the U50 program (Cock et al. 2009; Lutz 2013) 4
QUAST 2.3 Calculates assembly metrics (N50, N75, L50, GC%, etc.) based on the input contig file (Gurevich et al. 2013) 5