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View Code? Open in Web Editor NEWEliminating Assembly Gaps by Long read Extension
License: GNU General Public License v3.0
Eliminating Assembly Gaps by Long read Extension
License: GNU General Public License v3.0
Switch from manual temporary files to something like tmpnam.
The current configuration does not allow multiple instances of the scaffolder to run in the same folder.
It seems, graphmap have some problem with "align" flag. How to fix it ?
โ bin git:(master) โ ~/Tools/EAGLER/release/eagler -x ont -t 40 /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/EAGLER_SSPACED_out -g graphmap
[INPUT] Reading draft genome: /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta
[INPUT] Reading long reads: /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta
[ALIGNER] Initializing graphmap aligner...
[ALIGNER] Creating index...
ERROR: Unknown value of 'tool' parameter. Exiting.
Usage:
graphmap tool
Options
tool STR Specifies the tool to run:
align - the entire GraphMap pipeline.
owler - Overlapping With Long Erroneous Reads.
../vendor/seqan/include/seqan/basic/basic_exception.h:368 FAILED! (Uncaught exception of type std::runtime_error: command "graphmap -v 0 -I -r "/media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta"" failed with exit status 256)
[1] 46760 abort (core dumped) ~/Tools/EAGLER/release/eagler -x ont -t 40 -g graphmap
Edit Makefile.rules such that it recompiles all source files that depend on the edited header file.
Align reads to all contigs at the same time with one bwa command, with intent to reduce false positive alignments.
Automatically detect concurrency level and set BWA flag.
Fix linker error on -lrt flag on OS X. Find a way do discriminate OS in makefile rules.
Realign dropped reads to contig when coverage falls below acceptable value.
Rework SeqAn submodule configuration to avoid pulling the whole repository when installing the ONTscaffolder. Only the include
folder should be used.
Program creates multiple temporary files during execution. They should be stored in temporary folder.
Also, figure out a best way to handle temporary file paths in code.
Add doxygen documentation support.
Create a script to automatically test various implementations and parameters of the scaffolder.
List of small enhancements that need to be done:
Input parameters: pairs (start, end)
Meaning: remove genome subsequence [start, end] from reference genome
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