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biomedicalinformaticsgroup
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Sargasso
Sargasso disambiguates mixed-species high-throughput sequencing data.
http://biomedicalinformaticsgroup.github.io/Sargasso/
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sambamba sort fill up the /tmp quickly when running multiple thread of sorting
#62
hxin
closed
6 years ago
0
fix version number
#61
hxin
closed
6 years ago
0
fix version number
#60
hxin
closed
6 years ago
0
check_hits in hits_checker now uses the mim_mismatches instead of max_mismatches.
#59
hxin
closed
6 years ago
2
Deal with insertions and deletions wrt reference in CIGAR string
#58
lweasel
closed
6 years ago
3
Better define behaviour of _check_cigars() when multimaps allowed
#57
lweasel
closed
6 years ago
1
Inconsistent use of mismatches in thresholds
#56
lweasel
closed
6 years ago
1
Cope with unequal paired-end read lengths
#55
lweasel
closed
6 years ago
1
Xin add option for star executable #51
#54
hxin
closed
6 years ago
0
Fix edge case where no reads map for a species
#53
lweasel
closed
5 years ago
1
add options --delete-intermediate to delete intermediate BAMs including the raw mapped BAMs and the sorted BAMs.
#52
hxin
closed
6 years ago
0
Add option to specify location of STAR executable
#51
lweasel
closed
6 years ago
1
change Filtered-Hits/Filtered-Reads to Assigned-Hits/Assigned-Reads w…
#50
hxin
closed
6 years ago
0
use species name rather than a S0/S1 in the log file
#49
hxin
closed
6 years ago
0
Enhance filtering summary statistics
#48
lweasel
closed
5 years ago
4
Add a "permissive" startup option which only compares read mappings
#47
lweasel
closed
7 years ago
1
Overall filtering summary file only shows stats for last sample
#46
lweasel
closed
7 years ago
0
Update documentation for multispecies case
#45
lweasel
closed
7 years ago
0
Building STAR indexes hanging
#44
lweasel
closed
7 years ago
0
"species_separator -v" shows incorrect version info.
#43
lweasel
closed
7 years ago
0
Document external tool dependencies
#42
lweasel
closed
7 years ago
0
filter summary file appears to be broken
#41
s-heron
closed
8 years ago
1
Include paper analysis scripts
#40
lweasel
closed
5 years ago
0
Output overall stats and log files
#39
lweasel
closed
8 years ago
5
add debug option to follow specific reads through the filter process
#38
s-heron
closed
5 years ago
2
Change minmatch and mismatch threshold options to be proportions of read length
#37
lweasel
closed
8 years ago
0
Add option to control size of minimum exon alignment
#36
lweasel
closed
8 years ago
1
Remove --reject-edits option?
#35
lweasel
closed
8 years ago
2
Add in filter profiles
#34
s-heron
closed
8 years ago
3
Add option(s) for "conservative" filtering
#33
lweasel
closed
8 years ago
0
Possible issue with overhang criteria
#32
lweasel
closed
5 years ago
2
Change minmatch threshold option to max unmatched?
#31
lweasel
closed
8 years ago
1
Add real data tests
#30
lweasel
closed
7 years ago
2
Consider case when alignments span >2 exons
#29
lweasel
closed
8 years ago
2
Main script should convert paths in options to absolute paths
#28
lweasel
closed
8 years ago
1
Deal with single-end reads case
#27
lweasel
closed
8 years ago
0
Use docopt for command line processing in filter_control.py
#26
lweasel
closed
8 years ago
1
filtering output file concatenation
#25
s-heron
closed
8 years ago
1
ensure maintenance of BAM file compression
#24
s-heron
closed
8 years ago
2
sed extraction of read ids from sambamba stream slower than necessary
#23
s-heron
closed
8 years ago
0
Add option to control number of threads to be used
#22
lweasel
closed
8 years ago
2
Add option(s) to delete intermediate files during processing
#21
lweasel
closed
6 years ago
3
Add more logging at all stages
#20
lweasel
closed
5 years ago
0
Add step to Makefile to sort mapped reads in name order
#19
lweasel
closed
9 years ago
0
Parallelise "filter reads" step in Makefile
#18
lweasel
closed
8 years ago
2
Fill out map_reads script
#17
lweasel
closed
8 years ago
0
Add step to Makefile to remove "masked" reads
#16
lweasel
closed
6 years ago
1
Add step to Makefile to collate raw reads
#15
lweasel
closed
8 years ago
0
Write tool documentation
#14
lweasel
closed
8 years ago
2
Setup location for tool documentation on ReadTheDocs
#13
lweasel
closed
7 years ago
2
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