First retrimmed to remove 4 bp 5' and seqs shorter than 90 bp
robertsmac:novocraft sr320$ ./novoindex emtagseq_trim_all /Volumes/Bay3/Software/novocraft/data/EM_tagseqtrim.fa
# novoindex (2.8) - Universal k-mer index constructor.
# (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd
# novoindex emtagseq_trim_all /Volumes/Bay3/Software/novocraft/data/EM_tagseqtrim.fa
# Creating 4 indexing threads.
# Building with 13-mer and step of 1 bp.
# novoindex construction dT = 363.5s
# Index memory size 2.924Gbyte.
# Done.
--
robertsmac:novocraft sr320$ ./novoalign -f /Volumes/Bay3/Software/novocraft/data/EM2Atrim2.fa -d /Volumes/Bay3/Software/novocraft/data/emtagseq_trim_all -o SAM >/Volumes/Bay3/Software/novocraft/data/EM2Atrim2_align_all.SAN
# novoalign (V2.08.02 - Build Jun 28 2012 @ 17:02:48 - A short read aligner with qualities.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# novoalign.lic file not found.
# Licensed for evaluation, educational, and not-for-profit use only.
# novoalign -f /Volumes/Bay3/Software/novocraft/data/EM2Atrim2.fa -d /Volumes/Bay3/Software/novocraft/data/emtagseq_trim_all -o SAM
# Starting at Wed Nov 21 12:01:08 2012
# Interpreting input files as FASTA.
OUTPUT
---
Also aligning all trimmed fast on "all" index
robertsmac:novocraft sr320$ ./novoalign -f /Volumes/Bay3/Software/novocraft/data/EM_tagseqtrim.fa -d /Volumes/Bay3/Software/novocraft/data/emtagseq_trim_all -o SAM >/Volumes/Bay3/Software/novocraft/data/EM_all_align_all.sam
# novoalign (V2.08.02 - Build Jun 28 2012 @ 17:02:48 - A short read aligner with qualities.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# novoalign.lic file not found.
# Licensed for evaluation, educational, and not-for-profit use only.
# novoalign -f /Volumes/Bay3/Software/novocraft/data/EM_tagseqtrim.fa -d /Volumes/Bay3/Software/novocraft/data/emtagseq_trim_all -o SAM
# Starting at Wed Nov 21 12:19:49 2012
# Interpreting input files as FASTA.
