ibest ARC issues - Githubissues

ibest / ARC

Assembly by Reduced Complexity (ARC)

Apache License 2.0

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the contigs.fasta is empty

#57 houzhe1991 opened 6 years ago
0
while Patching BLAT，there is nothing /bin/x86_64 folder.

#56 SkyStarStear opened 6 years ago
0
In some rare cases, ARC thinks no reads have been recruited despite successful mapping

#55 samhunter opened 7 years ago
0
Retain Fastg output from Spades

#54 samhunter opened 8 years ago
1
How to set kmer value of spades in ARC config file?

#53 quxiaojian opened 8 years ago
2
Make a 1.1.3 release

#52 tseemann closed 8 years ago
1
ARC parameter parsing assumes parameters that start with a number are numeric

#51 magitz closed 8 years ago
2
ARC doesn't properly detect missing PE files

#50 samhunter closed 8 years ago
1
Bug with read recruitment when targets have an ARC-like name

#49 samhunter closed 8 years ago
1
Indexing is really slow.

#48 samhunter opened 9 years ago
0
enhancement request to deal with unusual read names in SRA datasets (causes KeyError termination)

#47 jayoung closed 8 years ago
11
Do a better job of detecting corrupted read indexes

#46 samhunter closed 8 years ago
1
"KeyError" on failed target assembly after previous iteration killed for that target

#45 atcg opened 9 years ago
3
Reduce disk space requirements when using bowtie2

#44 samhunter closed 8 years ago
4
Improve speed and reduce disk IO for read recruitment

#43 samhunter opened 9 years ago
0
Speed up SPAdes

#42 samhunter closed 8 years ago
2
Allow alternative working folder

#41 samhunter closed 10 years ago
1
Biopython method is deprecated

#40 samhunter closed 10 years ago
3
Add the ability to use high-specificity search on the first iteration

#39 samhunter closed 10 years ago
1
Enable simple repeat screening on iteration 1

#38 samhunter closed 10 years ago
1
Improve repeat detection

#37 samhunter opened 10 years ago
0
Generate more summary tables

#36 samhunter closed 10 years ago
1
idiot proof dependencies

#35 zeeev closed 10 years ago
2
Fatal -- missing module

#34 zeeev closed 10 years ago
2
bowtie2-build crashes if a contig is all 'n'

#33 samhunter closed 10 years ago
0
ARC sometimes incorporates a lot of off-target and/or repetative reads

#32 samhunter closed 10 years ago
1
Keep contigs from previous assembly if current assembly is killed

#31 samhunter closed 10 years ago
1
bowtie2 only writes reads to a single target

#30 samhunter closed 11 years ago
1
Make urt switch for Newbler dynamic

#29 samhunter closed 10 years ago
1
Log file is missing entries

#28 samhunter opened 11 years ago
0
Output Qual values for contigs

#27 samhunter opened 11 years ago
0
Fix bug in finished contigs out file

#26 samhunter closed 11 years ago
1
Allow ARC to resume a run if it is terminated/crashes

#25 samhunter opened 11 years ago
0
Do a better job of cleaning up intermediate files if ARC is restarted

#24 samhunter closed 11 years ago
1
Add support for gzipped files

#23 samhunter opened 11 years ago
2
SPAdes assembly fails on low coverage (<=10X) contigs (killing ARC)

#22 brantfaircloth closed 11 years ago
8
Update Install Requirement

#21 msettles closed 11 years ago
1
Fasta as input

#20 msettles closed 11 years ago
1
Modify map_against_reads behavior

#19 samhunter closed 11 years ago
1
If reads are mapped, but no contig is assembled, use the mapped reads for the next mapping step

#18 samhunter closed 11 years ago
1
Allow mapping against reads instead of contigs on first iteration

#17 samhunter closed 11 years ago
1
Generate mapping statistics

#16 samhunter closed 11 years ago
1
Handle the situation where no reads are mapped from an entire Sample

#15 samhunter closed 11 years ago
1
ARC is much too slow for very large sets of reads

#14 samhunter closed 11 years ago
1
Don't call assembler if no reads are mapped

#13 samhunter closed 11 years ago
1
Targets with names containing non-alphanumeric characters cause problems

#12 samhunter closed 11 years ago
1
If no files are written to the PE files or SE file, the assembler will crash

#11 samhunter closed 11 years ago
1
Check for idx file and don't re-index if it exists

#10 samhunter closed 11 years ago
1
Keep final set of assemblies

#9 samhunter closed 10 years ago
1
Refactor code for passing params

#8 samhunter closed 11 years ago
1