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Shamir-Lab
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Recycler
This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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Samtools sort changed
#46
termithorbor
closed
2 years ago
1
Update SPAdes home page link
#45
tfmorris
closed
3 years ago
0
AttributeError: Digraph object
#44
vappiah
closed
3 years ago
1
Visualizing the predicted plasmids
#43
vappiah
closed
3 years ago
1
Using contigs or scaffolds instead of the assembly graph.
#42
vappiah
closed
3 years ago
5
No output produced
#41
sum732
opened
4 years ago
3
recycler.py doesn't end (metagenome data)
#40
vjoliveira
closed
3 years ago
3
not an issue: small suggestion for recycler.py
#39
greytear
opened
4 years ago
0
Empty output files
#38
LPerlaza
closed
4 years ago
1
Support for GFA graph format?
#37
VadimDu
opened
4 years ago
0
''Node not found'' issue
#36
Ksalanin
closed
5 years ago
1
Continuing bug fix issue #33
#35
dpellow
closed
5 years ago
0
Bug fix for issue #33 - use correct k value for spades-like name
#34
dpellow
closed
5 years ago
1
Length of circular contigs
#33
Russel88
closed
5 years ago
6
Issue #29 Ensure no division by zero
#32
dpellow
closed
5 years ago
0
Recycler with Bowtie2 and MEGAHIT
#31
Russel88
closed
6 years ago
1
Support for assembly graphs in .gfa format
#30
caspargross
closed
5 years ago
3
ZeroDivisionError: float division by zero
#29
peng-ye
closed
5 years ago
2
RuntimeWarning: invalid value encountered in sqrt
#28
Freemacl
opened
6 years ago
5
ImportError: No module named recyclelib.utils
#27
gamer3051
opened
6 years ago
1
Create CITATION
#26
katrinleinweber
closed
6 years ago
2
Updates to tests, fix issue #20
#25
dpellow
closed
6 years ago
0
Bug fix for SPAdes latest version reverse complement node ordering
#24
dpellow
closed
6 years ago
0
Update choice of node and its reverse complements to reflect changes …
#23
dpellow
closed
6 years ago
0
RuntimeError: dictionary changed size during iteration
#22
JuanmaMedina
closed
6 years ago
2
make_fasta_from_fastg.py :: incorrect help message
#21
EricDeveaud
closed
6 years ago
1
test
#20
tandler
closed
6 years ago
1
Fix bug issue #17: cast isolates iterator to list for networkX 2.0
#19
dpellow
closed
6 years ago
0
make_fasta_from_fastg.py: error: argument -b/--bam is required
#18
thanhleviet
closed
6 years ago
1
Recycle.py: Runtime error
#17
Freemacl
closed
6 years ago
8
Update to prevent division errors and version patch
#16
cameronmartino
closed
6 years ago
0
minor typo in 'Preparing the BAM input:'
#15
cameronmartino
closed
5 years ago
1
error after running recycle.py
#14
OAF12
opened
6 years ago
8
Update README and add output directory option to recycle.py
#13
fmaguire
closed
6 years ago
0
Minor fixes/enhancement
#12
fmaguire
closed
6 years ago
2
output sequence fasta
#11
EmilyHoedt
closed
6 years ago
5
mapping input contig names to output
#10
lskatz
opened
7 years ago
6
error creating the BAM file
#9
Niazevedo
opened
7 years ago
1
best assembler for the job?
#8
lskatz
opened
7 years ago
1
fix the ambiguity problem of package name "recycle" and script "recycle.py"
#7
shenwei356
closed
7 years ago
0
make_fasta_from_fastg.py
#6
rprops
closed
7 years ago
14
I have a problem when I used recycler
#5
OAF12
closed
7 years ago
3
Packing the code
#4
druvus
closed
7 years ago
6
Fastg file
#3
fabianomenegidio
closed
7 years ago
1
Adding shebang line to recycler.py
#2
druvus
closed
8 years ago
1
recycler output
#1
cytang19
closed
8 years ago
2