Alignment test: 25 sequences against HG19

>time ./novoalign -d genome/hg19.nix -f read/test.txt >hello.txt

real 0m29.149s

user 0m5.610s

sys 0m2.990s

>less hello.txt

# novoalign (2.06.09MT - Jun 16 2010 @ 12:36:05) - A short read aligner with qualities.

# (C) 2008 NovoCraft

# Licensed for evaluation, educational, and not-for-profit use only.

# novoalign -d genome/hg19.nix -f read/test.txt

# Interpreting input files as Illumina FASTQ, Cassava Pipeline 1.3.

# Index Build Version: 2.6

# Hash length: 13

# Step size: 2

@HWI-EAS240_0001:7:1:1086:16499#0/1 S TGTTTTCCTGNCAGCCCCCACCTTTTTAGTACATGTCTCATCCTACTGCTGTTTNNNGGATTGTGAATGTGTATTN BBBBB@?@@@#::82;8;889:=@BB>@>*?*?+5:;3@7>@(@78@

......

############################### NM

# Read Sequences: 25

# Aligned: 0

# Unique Alignment: 0

# Gapped Alignment: 0

# Quality Filter: 1

# Homopolymer Filter: 0

# Elapsed Time: 0,139s

# Done.