Noob here,
I'm trying to map a file of contigs and scaffolds onto a reference genome but bowtie keeps outputting the same error:
bowtie2 -f -x wmel_genome -U ~/Aa23/ref/assemblies/wMelPopPGYP.finalassembly-alt.fasta
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
(ERR): bowtie2-align died with signal 6 (ABRT)
I edited my file from a non-fasta so that every contig/scaffold sequence began with ">scaffold/contig-name". There are over 15 separated sequences in the file. Some of the sequences contain "n" character I'm guessing for uncertain/missing nucleotides.
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written
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YOUSEUFS •
4 answers
I find bwa mem is useful for this case and have used it many times. Bowtie2 is not suitable.
I would use samtools, not picard, for the SAM-> bam conversion, as Picard gets messed up by very long MD strings from long contigs
Minimap2 should also be able to do this job.
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