Comparison of re-called Albacore and Flappie sequences from E. coli K-12 MG1655
Description
I used the first few (545) original Fast5 files from Nick Loman's ultra-long read E. coli K-12 MG1655 R9.4 sequencing run. See the blog post here. Direct link to the complete fast5 dataset here.
Program versions:
* Albacore 2.1.10
* Flappie 1.0.0-0048dfd
The example alignment was carried out using seaview (1:4.6.1.2-2), and visualised using spiralign from my bioinfscripts repository (see source code in this archive):
$ spiralign.r -size 2000x2000 -noalign -noborder -loops 12.75 -outfmt png -type nucl -title "Flappie vs Albacore\n(Ecoli_MG1655)" aligned_all_ddea.fa
Flappie was distributed across multiple processing threads using GNU parallel:
$ ls Ecoli_MinKNOW_1.4_RAD002_Sambrook/0/nanopore2_20170301_FNFAF09967_MN17024_mux_scan_170301_MG1655_PC_RAD002_76964_ch* | parallel --group -j 10 -L 1 ~/install/flappie/flappie | gzip > called_flappie_Ecoli_MinKNOW_1.4_RAD002_Sambrook.fq.gz
Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.
