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bergmanlab
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ngs_te_mapper
Software for detecting transposable element insertions from next-generation sequencing data
BSD 3-Clause "New" or "Revised" License
14
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6
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add support for multithreading
#23
shunhuahan
closed
5 years ago
0
rename insertion types in bed files
#22
cbergman
closed
1 year ago
0
Remove legacy output and code
#21
cbergman
closed
1 year ago
1
Change the TE database location
#20
cbergman
closed
9 years ago
1
Recode R scripts to allow full paths for input files
#19
cbergman
closed
9 years ago
1
Refactor example sequences
#18
cbergman
closed
9 years ago
1
Add test to check that user generated output matches expected results
#17
cbergman
closed
9 years ago
1
Change mapping engine from BLAT to BWA
#16
cbergman
closed
9 years ago
1
Add ability to make predictions based on paired-end information
#15
cbergman
closed
3 years ago
0
Add the ability to get insertions from sam files
#14
raquel-linheiro
closed
10 years ago
3
recode fasta extraction from first psl result
#13
raquel-linheiro
closed
9 years ago
1
include fastq to fasta conversion so system takes fastq as input
#12
raquel-linheiro
closed
9 years ago
1
Add ability to identify if TEs in reference genome are present in sample
#11
cbergman
closed
1 year ago
3
add citation file
#10
cbergman
closed
10 years ago
1
add license
#9
cbergman
closed
10 years ago
1
Add support to use blasr or bwa mem as mapping engine for PacBio reads
#8
cbergman
closed
1 year ago
1
Do not keep reads that are ambigously mapping to start or end of the TE
#7
raquel-linheiro
closed
9 years ago
2
Update system to allow multiple input files
#6
nelson42
closed
11 years ago
0
Add extensions to output files where necessary
#5
raquel-linheiro
closed
11 years ago
0
Update readme to explain inputs and output of system
#4
raquel-linheiro
closed
1 year ago
1
adapt TSD finding code to allow data from pooled individuals
#3
cbergman
closed
1 year ago
0
update reference genome in example script to be UCSC compliant
#2
cbergman
closed
11 years ago
1
update test data to have valid ENA identifiers
#1
cbergman
closed
11 years ago
1