galaxyproject dunovo issues

galaxyproject / dunovo

Reference-free duplex sequencing pipeline.

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issues

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Trimmer.py documentation

#33 haiderinam opened 2 years ago
0
Suboptimal alignment between strands

#32 NickSto closed 2 years ago
0
Bug in consensus sequence calling

#31 NickSto closed 2 years ago
0
Surface correct.py --allow-no-nm-if-ns in Galaxy

#30 NickSto opened 2 years ago
0
Change defaults in 3.0

#29 NickSto opened 2 years ago
1
align-families.py stalls on some inputs

#28 NickSto opened 2 years ago
0
bowtie output sometimes lacks NM tag

#27 NickSto opened 3 years ago
0
Add dependency on samtools; update networkx ver

#26 afgane opened 3 years ago
0
Random barcode choices in correct.py

#25 NickSto opened 3 years ago
0
Please document switch to python3

#24 dpryan79 opened 3 years ago
1
"Could not locate a Bowtie index corresponding to basename "refdir/barcodes-ref"

#23 jmath97 opened 3 years ago
1
QC pipeline: Get all tools deployed on Galaxy Main

#22 NickSto opened 4 years ago
0
QC pipeline: Trim ends of reads

#21 NickSto opened 4 years ago
1
QC pipeline: Double-counting variants in overlapping mates

#20 NickSto opened 4 years ago
1
More intelligently identify barcode sequence, based on 5bp linker after it.

#19 NickSto opened 5 years ago
0
Sequence Content Trimmer tool output names are ambiguous

#18 NickSto opened 6 years ago
0
Make consensus reads tool output fastq, not fastqsanger

#17 NickSto opened 6 years ago
0
Printing empty consensus reads

#16 NickSto closed 6 years ago
2
Correct Barcode tool error - networkx-related

#15 thi-trinh opened 6 years ago
2
make-consensi.py AssertionError on bad input

#14 NickSto opened 6 years ago
0
Awk shared library error on main

#13 NickSto closed 6 years ago
2
not needed anymore and causes more trouble that it solves

#12 bgruening closed 2 years ago
5
tool_dependencies.xml: Compilation fails because of missing kalign submodule.

#11 NickSto closed 6 years ago
1
align_families.py: Incomplete output in Galaxy

#10 NickSto opened 6 years ago
0
align_families.py: MAFFT memory leak

#9 NickSto opened 6 years ago
0
dunovo.py: Sequence length mismatch

#8 NickSto opened 6 years ago
0
align_families.py: Kalign memory leak

#7 NickSto opened 6 years ago
2
align_families.py: Kalign crash on short reads

#6 NickSto closed 6 years ago
2
Barcode correction: Set allowed edit distance during bowtie2 alignment as well as in correct.py

#5 NickSto closed 6 years ago
1
More sensical output for dunovo.py (eliminate need for outconv.py)

#4 NickSto closed 7 years ago
1
dunovo.py: Separate outputs for lone SSCSs vs. paired ones (that produce a DCS)

#3 NickSto opened 7 years ago
0
Add parameter for consensus calling: # of reads which must contain the base

#2 NickSto closed 7 years ago
1
Add parameter for consensus calling: % of reads which must contain the base

#1 NickSto closed 7 years ago
1