Release Notes PhyResSE

• 10-11-15 PhyResSE 1.0, component versions:
  • jQuery JavaScript Library v1.9.1
  • jQuery UI - v1.10.3
  • libStatGen v1.0.10
  • FastQValidator v0.1.1
  • Blast v2.2.26
  • Ref. Genome: NC_000962.3
  • FastQC v0.10.1
  • QualiMap v0.7.1
  • BWA v0.7.4
  • SAMtools v0.1.19
  • picard-tools v1.94
  • Genome Analysis TK 2.5-2-gf57256b
  • VCFtools v0.1.12b
  • tabix v0.2.5 (r1005)
  • vcf_tab_to_fasta_alignment.pl by Christina Bergey (Bergey CM (2012). vcf-tab-to-fasta; http://code.google.com/p/vcf-tab-to-fasta)
  • FastTree v2.1.8 as multi-threaded executable (+SSE +OpenMP)
  • jstree (no versioning found, from http://lh3lh3.users.sourceforge.net/jstree.shtml)
• 20-10-15 Update Resi-List-Master.v27:
  • 124 phylogenetic SNP from Coll et al. 2014 added
    Genome position: 5520; 6112; 6124; 7222; 7892; 8040; 8452; 8876; 9260; 9566; 9611; 62657; 107794; 346693; 355181; 403364; 497491; 514245; 541048; 615614; 615938; 762434; 763031; 763884; 763886; 764013; 764995; 765150; 765171; 765230; 766955; 783601; 797736; 874787; 891756; 931123; 1084911; 1132368; 1137518; 1237818; 1416410; 1416702; 1416977; 1417019; 1455780; 1472337; 1487796; 1491275; 1501468; 1502120; 1719757; 1759252; 1799921; 1816587; 1834916; 1850119; 1881090; 1882180; 1918281; 2101921; 2102218; 2102990; 2155503; 2411730; 2505085; 2518919; 2622402; 2694560; 2831482; 2874344; 2875883; 3021283; 3216553; 3273107; 3388166; 3466426; 3470377; 3479545; 3513538; 3514512; 3570528; 3722702; 3836274; 3836739; 3977226; 4125058; 4151558; 4229087; 4238120; 4238778; 4238963; 4239298; 4239843; 4240153; 4240897; 4241042; 4241562; 4242643; 4242883; 4243848; 4244420; 4245055; 4245969; 4246088; 4246508; 4246864; 4246930; 4248073; 4248115; 4249012; 4249732; 4260268; 4268928; 4269351; 4269375; 4307886; 4316114; 4326176; 4326439; 4326739; 4328004; 4398141; 4404247; 4407780
• 20-10-15 Update Resi-List-Master.v26:
  • Erroneous WT and mutant bases corrected
    Genome position: 6734 WT a mutant g; 761154 WT t mutant g; 4247513 WT t mutant c
• 07-07-15 Update Resi-List-Master.v25:
  • 137 high confidence PZA resistance mediating SNPs added
    Genome position: 2288683; 2288697; 2288703; 2288703; 2288718; 2288719; 2288740; 2288752; 2288754; 2288761; 2288764; 2288772; 2288772; 2288778; 2288779; 2288805; 2288806; 2288817; 2288817; 2288818; 2288823; 2288826; 2288827; 2288828; 2288830; 2288832; 2288832; 2288833; 2288838; 2288839; 2288841; 2288847; 2288847; 2288848; 2288853; 2288853; 2288857; 2288868; 2288869; 2288874; 2288880; 2288883; 2288883; 2288886; 2288886; 2288887; 2288887; 2288895; 2288895; 2288920; 2288920; 2288928; 2288930; 2288931; 2288933; 2288934; 2288935; 2288938; 2288944; 2288944; 2288945; 2288952; 2288952; 2288954; 2288955; 2288955; 2288956; 2288957; 2288960; 2288960; 2288961; 2288961; 2288962; 2288971; 2288988; 2288997; 2288998; 2289000; 2289000; 2289001; 2289028; 2289029; 2289030; 2289038; 2289038; 2289039; 2289043; 2289050; 2289057; 2289068; 2289068; 2289070; 2289071; 2289072; 2289072; 2289081; 2289081; 2289082; 2289089; 2289090; 2289090; 2289091; 2289097; 2289100; 2289100; 2289103; 2289111; 2289133; 2289138; 2289140; 2289150; 2289162; 2289171; 2289180; 2289186; 2289193; 2289200; 2289202; 2289203; 2289206; 2289207; 2289214; 2289218; 2289219; 2289220; 2289222; 2289223; 2289225; 2289231; 2289234; 2289239; 2289240; 2289240; 2289248; 2289248; 2289252; 2289252
• 12-06-15 Update Resi-List-Master.v24:
  • embC T270I removed from EMB resistance
• 02-06-15 All samples of the session summarized by exports (VCF, FASTA, VCF-stats, VCF-tab, ML-tree, variants)
• 27-05-15 Illumina 1.5 and older data supported
• 16-04-15 Upload: automatically renaming
  • default filenames directly from sequencer (..._R1_001.fastq.gz ⇒ ..._001_R1.fastq.gz),
  • # ⇒ _hash_ (# as part of a file name works for all our scripts but not as part of a URL, therefore results were not shown!)
• 25-03-15 Ion Torrent data supported (metaphyresse.v8.txt, diff)

• 16-07-14 Start keeping release records,
  starting from Resi-List-Master.v18.txt and metaphyresse.v7.txt.