User contributions
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- 10:40, 27 July 2016 (diff | hist) . . (+129) . . BUSCO
- 10:31, 27 July 2016 (diff | hist) . . (+196) . . BUSCO
- 10:02, 27 July 2016 (diff | hist) . . (+22) . . BUSCO
- 10:00, 27 July 2016 (diff | hist) . . (+58) . . BUSCO
- 18:31, 26 July 2016 (diff | hist) . . (+238) . . BUSCO
- 18:30, 26 July 2016 (diff | hist) . . (+1) . . Augustus
- 18:29, 26 July 2016 (diff | hist) . . (+245) . . Augustus
- 17:25, 26 July 2016 (diff | hist) . . (+18) . . Augustus
- 15:39, 26 July 2016 (diff | hist) . . (+222) . . N Augustus (Created page with "= Introduction = Worthy gene prediction program from Mario Stanke at Greifenswald. = Admin notes only= == Compilation == Is a simple "make" but the Makefiles (especially t...")
- 15:37, 26 July 2016 (diff | hist) . . (+15) . . Main Page
- 13:05, 26 July 2016 (diff | hist) . . (+10) . . BUSCO
- 11:09, 22 July 2016 (diff | hist) . . (+302) . . BUSCO
- 11:04, 22 July 2016 (diff | hist) . . (+340) . . N BUSCO (Created page with "= Introduction = BUSCO, like Cegma, is a special tool for the field of "completeness assessment". This concerns genome assemblies, particularly ones generated de-novo, when b...")
- 10:57, 22 July 2016 (diff | hist) . . (+12) . . Main Page
- 17:13, 21 July 2016 (diff | hist) . . (-2) . . Cegma (current)
- 17:11, 21 July 2016 (diff | hist) . . (+5,160) . . N Cegma (Created page with " = How to use Cegma= By default, Cegma expects that you will only analyse one fasta sequence each time. So it has certain standard names for its output files which '''do not...")
- 17:09, 21 July 2016 (diff | hist) . . (+12) . . Main Page
- 08:18, 20 July 2016 (diff | hist) . . (+103) . . Srst2
- 17:13, 19 July 2016 (diff | hist) . . (+10) . . Srst2
- 17:12, 19 July 2016 (diff | hist) . . (+825) . . Srst2
- 16:55, 19 July 2016 (diff | hist) . . (+95) . . Srst2
- 15:59, 19 July 2016 (diff | hist) . . (+18) . . Srst2
- 15:58, 19 July 2016 (diff | hist) . . (-35) . . Srst2
- 15:50, 19 July 2016 (diff | hist) . . (+182) . . Srst2
- 15:15, 19 July 2016 (diff | hist) . . (+42) . . Patric (→Introduction) (current)
- 15:15, 19 July 2016 (diff | hist) . . (+754) . . N Patric (Created page with "= Introduction = = Guide = * Registering for Patric is a good idea. * When browsing you have an implicit workspace. You add items to it if you are interested in them. * The...")
- 15:07, 19 July 2016 (diff | hist) . . (+1) . . Main Page
- 15:07, 19 July 2016 (diff | hist) . . (+50) . . Main Page
- 18:01, 18 July 2016 (diff | hist) . . (+92) . . Miseq Prokaryote FASTQ analysis (current)
- 17:47, 18 July 2016 (diff | hist) . . (+22) . . Miseq Prokaryote FASTQ analysis
- 17:46, 18 July 2016 (diff | hist) . . (+262) . . Miseq Prokaryote FASTQ analysis
- 17:43, 18 July 2016 (diff | hist) . . (+9) . . Miseq Prokaryote FASTQ analysis
- 17:40, 18 July 2016 (diff | hist) . . (+20) . . Miseq Prokaryote FASTQ analysis
- 17:29, 18 July 2016 (diff | hist) . . (+2) . . Miseq Prokaryote FASTQ analysis
- 17:27, 18 July 2016 (diff | hist) . . (+11) . . Miseq Prokaryote FASTQ analysis
- 17:26, 18 July 2016 (diff | hist) . . (+2) . . Miseq Prokaryote FASTQ analysis
- 17:24, 18 July 2016 (diff | hist) . . (+571) . . Miseq Prokaryote FASTQ analysis
- 17:16, 18 July 2016 (diff | hist) . . (0) . . Miseq Prokaryote FASTQ analysis
- 17:15, 18 July 2016 (diff | hist) . . (+581) . . N Miseq Prokaryote FASTQ analysis (Created page with "=Introduction= We have our own Miseq machine and each week a run is carried out (each run costs about £1000 in consumibles) from various samples. They are unloaded onto HDR...")
- 17:09, 18 July 2016 (diff | hist) . . (+38) . . Main Page
- 17:55, 13 July 2016 (diff | hist) . . (+3) . . Srst2
- 18:39, 7 July 2016 (diff | hist) . . (+169) . . SPAdes
- 16:43, 6 July 2016 (diff | hist) . . (+2,538) . . FASTQC and MultiQC
- 16:43, 6 July 2016 (diff | hist) . . (+183) . . FASTQC and MultiQC
- 16:32, 6 July 2016 (diff | hist) . . (+5,010) . . N FASTQC and MultiQC (Created page with "=Introduction= Quality visualization = Help file = SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c...")
- 16:32, 6 July 2016 (diff | hist) . . (+12) . . Main Page
- 15:44, 6 July 2016 (diff | hist) . . (+1) . . FASTQC (current)
- 15:44, 6 July 2016 (diff | hist) . . (+1) . . FASTQC
- 15:43, 6 July 2016 (diff | hist) . . (-7) . . FASTQC
- 15:43, 6 July 2016 (diff | hist) . . (+5,015) . . N FASTQC (Created page with "=Introduction= Quality visualization = Help file = SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]...")
- 15:42, 6 July 2016 (diff | hist) . . (+13) . . Main Page
- 18:17, 5 July 2016 (diff | hist) . . (+317) . . Trimmomatic (current)
- 18:06, 5 July 2016 (diff | hist) . . (+53) . . Trimmomatic
- 18:05, 5 July 2016 (diff | hist) . . (+171) . . Trimmomatic
- 15:54, 5 July 2016 (diff | hist) . . (+550) . . Trimmomatic
- 18:01, 2 July 2016 (diff | hist) . . (-3) . . SPAdes
- 18:01, 2 July 2016 (diff | hist) . . (+126) . . SPAdes
- 16:36, 2 July 2016 (diff | hist) . . (+149) . . SPAdes
- 17:47, 1 July 2016 (diff | hist) . . (+735) . . SPAdes
- 17:16, 1 July 2016 (diff | hist) . . (+613) . . SPAdes
- 14:57, 30 June 2016 (diff | hist) . . (-2) . . Calculating coverage
- 14:53, 30 June 2016 (diff | hist) . . (+40) . . Calculating coverage
- 14:03, 30 June 2016 (diff | hist) . . (+663) . . Calculating coverage
- 17:12, 29 June 2016 (diff | hist) . . (+324) . . N Trimmomatic (Created page with "=Introduction= = Example use-cases= java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_pai...")
- 17:03, 29 June 2016 (diff | hist) . . (+18) . . Main Page
- 16:19, 29 June 2016 (diff | hist) . . (+164) . . 6TB storage expansion
- 16:05, 29 June 2016 (diff | hist) . . (+1,183) . . 6TB storage expansion
- 15:37, 29 June 2016 (diff | hist) . . (+754) . . 6TB storage expansion
- 15:28, 29 June 2016 (diff | hist) . . (+571) . . 6TB storage expansion
- 14:54, 29 June 2016 (diff | hist) . . (+90) . . 6TB storage expansion
- 14:50, 29 June 2016 (diff | hist) . . (+2) . . 6TB storage expansion
- 14:48, 29 June 2016 (diff | hist) . . (+3,259) . . 6TB storage expansion
- 14:42, 29 June 2016 (diff | hist) . . (+87) . . 6TB storage expansion
- 14:38, 29 June 2016 (diff | hist) . . (+7) . . 6TB storage expansion
- 14:38, 29 June 2016 (diff | hist) . . (+1,892) . . 6TB storage expansion
- 12:24, 29 June 2016 (diff | hist) . . (-1) . . 6TB storage expansion
- 12:13, 29 June 2016 (diff | hist) . . (+21) . . Samtools
- 12:06, 29 June 2016 (diff | hist) . . (+84) . . Samtools
- 10:57, 29 June 2016 (diff | hist) . . (+124) . . Samtools
- 10:32, 29 June 2016 (diff | hist) . . (+310) . . Samtools
- 18:31, 28 June 2016 (diff | hist) . . (-4) . . Main Page
- 18:23, 28 June 2016 (diff | hist) . . (-130) . . 6TB storage expansion
- 18:23, 28 June 2016 (diff | hist) . . (+226) . . 6TB storage expansion
- 17:53, 28 June 2016 (diff | hist) . . (+48) . . Calculating coverage
- 17:48, 28 June 2016 (diff | hist) . . (+300) . . N Calculating coverage (Created page with "= Introduction = Coverage can be calculated in several different ways and this pages aims to describe a few of them = Bedtools genomecov = This is one of the most commonly...")
- 17:16, 28 June 2016 (diff | hist) . . (+216) . . Main Page
- 13:42, 28 June 2016 (diff | hist) . . (+18) . . CallSNPs.py
- 14:35, 27 June 2016 (diff | hist) . . (+26) . . Samtools
- 14:18, 27 June 2016 (diff | hist) . . (-359) . . Main Page
- 14:17, 27 June 2016 (diff | hist) . . (+346) . . Main Page
- 16:21, 23 June 2016 (diff | hist) . . (+85) . . 6TB storage expansion
- 16:19, 23 June 2016 (diff | hist) . . (+111) . . 6TB storage expansion
- 16:14, 23 June 2016 (diff | hist) . . (+241) . . 6TB storage expansion
- 16:12, 23 June 2016 (diff | hist) . . (+58) . . 6TB storage expansion
- 16:04, 23 June 2016 (diff | hist) . . (+309) . . 6TB storage expansion (→= interpreter)
- 15:55, 23 June 2016 (diff | hist) . . (+161) . . 6TB storage expansion
- 15:45, 23 June 2016 (diff | hist) . . (+5,102) . . N BamQC (Created page with "= Introduction = From S. Andrews' lab, who also produce FastQC = Helpfile output = BamQC - A high throughput mapped sequence QC analysis tool SYNOPSIS ba...") (current)
- 15:44, 23 June 2016 (diff | hist) . . (+12) . . Main Page
- 15:32, 23 June 2016 (diff | hist) . . (+14) . . Main Page
- 14:48, 23 June 2016 (diff | hist) . . (+45) . . 6TB storage expansion
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