BIRCHv3.50

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Mystica Arrow set (with deep) 1.png [return to Release To Do List]


Contents

BIRCH

Upgrade to Java 1.8

BioLegato 1.0.4 - recompiled using Java 1.8

  • Can flamingo and albacore be upgraded to Java 1.7?

Introducing blreads

http://www.ccb.jhu.edu/software/hisat/index.shtml

Testing

Dataset: Genome tutorial

Linux Mac OSX
brassica (16 Gb) flamingo ccxx peacock (8 Gb) aliana (8 Gb)
Genome
Trimmomatic + + +
trim_galore + + +
pollux + + +
SOAPdenovo2 + NA NA
ABySS + + +
Spades + through K55 through K55
Quast + + +

Dataset: Transcriptomics tutorial

Linux Mac OSX
brassica (16 Gb) flamingo ccxx peacock (8 Gb) aliana (8 Gb)
Transcriptome
Trimmomatic + +
trim_galore + + +
Rcorrector + + +
SOAPdenovo-Trans + NA NA
Trinity + NA NA
RNASpades + through K49
transrate + +

Dataset: Differential expression tutorial

Linux Mac OSX
brassica (16 Gb) flamingo ccxx peacock (8 Gb) aliana (8 Gb)
Differential Expression
gff2gtf + +
extract exons + +
extract splice sites + +
Hisat2-build + +
Hisat2 + +
stringtie + +
stringtie merge + +
gffcompare + +
stringtie -B + +

BLAST/FASTA overhall

blpalign

Turns out there is no problem with phylogeny. The problem was that the alignment began with terminal gaps, and the Phylip programs require no terminal gaps. This is documented in the tutorial, but maybe we should add some sort of pre-scan that informs the user if the sequence begin with terminal gaps.

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