Activity for CG-Pipeline
-
Lee Katz committed [r705]
added a way for the highest score to be Z inste...
-
fixed a newline bug
-
put a die statement and explanation for a weird...
-
added a tag prefix warning
-
fixed a bug on combining quality scores. I THI...
-
script will now fail if the wrong options are p...
-
new consensus score is calculated based on dupl...
-
changed the quality scores to near-perfect for ...
-
added length parameter back. Get best quality r...
-
added ability to read stdin and also refactored...
-
fixed a bug where it wouldn't work for SE bam f...
-
added more phast functionality
-
new phast entry
-
defline changes
-
script to update phast database locally
-
checking if certain fields are defined
-
cloning features by the Clone perl semi-core mo...
-
CG-Pipeline released /cgp-v0.4.3.unstable.tar.gz
-
changed the VF database to the CP one
-
added numcpus for annotation
-
adding in better notes for uniprot
-
formatted the deflines for vfdb
-
more stable. Better checking for EC numbers. Ge...
-
better usage statement
-
added numcpus options
-
made reading the crispr gff more robust
-
tRNAscan-SE is optional
-
a script to detect PE fastq sequences
-
a script to filter out bad contigs
-
Added a little more robustness into signalp
-
added in gzipped output and additional help in ...
-
fixed a syntax bug
-
added better usage examples
-
buffering sequences before writing them. Hopef...
-
added EC numbers and an option to keep entries ...
-
better usage statement
-
better uniprot parsing and downloading
-
added gene clustering. Very similar to Prokka
-
made the deflines more simplified. Idea borrowe...
-
fixed the pdb command
-
made 'fast' apply to spades too, by restricting...
-
gam-create now prints to stderr so that it does...
-
-
Added a warning if the IS database is not present
-
removed is databases due to takedown notice fro...
-
should just warn instead of die if the assembly...
-
updated combiner a little more. It is still a ...
-
fixed contig matching a bit in glimmer and gene...
-
added prediction_min_predictors_to_call_orf as ...
-
added numcpus option in blast
-
prodigal gene prediction is now being checked
-
removed a data dumper
-
added numcpus option to prediction
-
reference assembly fixed a little bit more
-
fix on the estimated genome size for mapping il...
-
made the ngs merger redirect to the correct out...
-
fixed numcpus and estimatedGenomeSize parameters
-
added numcpus parameter for illumina
-
added numcpus option
-
made ngs-gam optional using a warning
-
made ngs-gam optional using a warning
-
added an --auto option to make it easier. Expe...
-
added better error messages and usage statements
-
now changes dots to Ns in sequences in case the...
-
added a 'perl' before fastqqc to ensure the cor...
-
more arg-annot
-
arg-annot blasting instead of card
-
arg-annot
-
ARG-ANNOT database
-
ngs merger
-
added spades to the illumina assembly
-
Added a couple more descriptions; added module ...
-
checkPrereqs now has descriptions of software, etc
-
checkPrereqs is checking prereqs slightly diffe...
-
fixed the example a bit
-
contig lengths are an output option
-
made the output for help and for assembly score...
-
rounding assembly score to 1000s place
-
works with >1 reads file. Still only works wit...
-
works with two assemblies now. Finished all ba...
-
A new assembly merger based on Illumina reads
-
fixed some random things in the script like the...
-
I think that spades is working for de novo asse...
-
fixed the number bug in chooseBest for assembly...
-
fixed a bug in the assembly metrics call
-
adding spades in this temporary script before m...
-
added skip parameter for annotation
-
added a strict threshold for CARD database
-
added temporary directory to run_annotation_bla...
-
fixed a bug in update_uniprot
-
added concatenation option
-
fixed the SRA PE detection method a little to m...
-
I forgot that this was renamed so it must be de...
-
filter uniprot script added... again?
-
incorporated the uniprot filtering to the updat...
-
add a way to filter uniprot fasta file
-
filter uniprot script for keeping bacteria only
-
GC content
1
