JoseBlanca franklin issues

JoseBlanca / franklin

franklin library for NGS sequencing analysis.

http://bioinf.comav.upv.es/franklin/

GNU Affero General Public License v3.0

25 stars 3 forks source link

issues

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Samtools fails if reference file has empty lines

#54 necrolyte2 opened 11 years ago
1
edge_trim not working

#53 xapple closed 11 years ago
1
evalua phobos for ssr

#52 JoseBlanca opened 12 years ago
0
Feature name generation should't be in gff writer

#51 pziarsolo opened 12 years ago
0
Remove tmp files on crash

#50 pziarsolo opened 13 years ago
0
take a look at btrim

#49 JoseBlanca opened 13 years ago
1
improve EST mapping to genome

#48 JoseBlanca opened 13 years ago
2
max_maf should be None by default

#47 JoseBlanca closed 13 years ago
1
seqio should be able to double encode solid

#46 JoseBlanca closed 13 years ago
1
create an annotation tool

#45 JoseBlanca opened 13 years ago
0
add cleaning report

#44 JoseBlanca opened 13 years ago
0
add contamination removal

#43 JoseBlanca opened 13 years ago
0
add default adaptors to clean_reads

#42 JoseBlanca opened 13 years ago
0
include univec with the distribution

#41 JoseBlanca closed 13 years ago
2
setuptools

#40 JoseBlanca opened 13 years ago
0
take a look at cutadapt

#39 JoseBlanca opened 13 years ago
0
take a look at freebayes

#38 JoseBlanca opened 13 years ago
0
Take a look at fastq screen

#37 JoseBlanca opened 13 years ago
0
mask repetitive before SNP calling

#36 JoseBlanca opened 13 years ago
0
add support for paired-ends

#35 JoseBlanca opened 13 years ago
0
take a look at the short adaptors clean code

#34 JoseBlanca closed 13 years ago
1
include java tools in the third party package

#33 JoseBlanca closed 13 years ago
1
Clear error messages

#32 JoseBlanca closed 13 years ago
1
add parameters to the log

#31 JoseBlanca opened 13 years ago
0
Remove old files

#30 JoseBlanca opened 13 years ago
1
sometimes when the cleaning fails the clean file remains

#29 JoseBlanca closed 13 years ago
1
blast+ install

#28 pziarsolo closed 13 years ago
1
Bam stats using a lot of memory

#27 pziarsolo closed 13 years ago
1
Remove short adapter

#26 pziarsolo closed 13 years ago
2
Bug : Orf annotation marks all orfs as reverses.

#25 pziarsolo closed 13 years ago
1
Too long cleaned 454 reads

#24 JoseBlanca closed 13 years ago
1
fix logging in tests

#23 JoseBlanca closed 13 years ago
1
do not import matplotlib in setup.py

#22 JoseBlanca closed 13 years ago
1
allow adaptor removal on solid reads

#21 JoseBlanca opened 13 years ago
0
Bugfix in boxplot graphic

#20 pziarsolo closed 13 years ago
1
correct 454 homopolymers using illumina

#19 pziarsolo opened 13 years ago
0
add stats for the assembly

#18 JoseBlanca closed 13 years ago
1
put unigenes in the correct direction

#17 JoseBlanca opened 14 years ago
0
annotate polyA

#16 JoseBlanca opened 14 years ago
0
Force snv filters to check again althougth the filters is already passed

#15 pziarsolo opened 14 years ago
0
release script creates a tar explosion

#14 JoseBlanca closed 14 years ago
1
Do not install unecessary scripts

#13 JoseBlanca closed 14 years ago
1
Vector database for cleaning should be optional

#12 pziarsolo closed 14 years ago
0
Create symlink instead of relative ones

#11 JoseBlanca closed 14 years ago
0
Use SSAHA as the default aligner for the long sequences

#10 JoseBlanca closed 13 years ago
1
Add some global statistics to the statisticis file

#9 JoseBlanca closed 14 years ago
1
write restriction enzymes in the vcf file

#8 JoseBlanca closed 14 years ago
1
improve memory on snv data structure

#7 JoseBlanca closed 14 years ago
1
centralize configuration parameter tweaking in one function

#6 JoseBlanca closed 13 years ago
1
SSR statistics

#5 JoseBlanca closed 14 years ago
1