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Table 1 Software versions and parameters used to generate the results

From: SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Software Version Parameters
HISAT2 2.0.4 –max-intronlen 300000 –novel-splicesite-
   outfile {output.novel_splice}
HISAT2_2PASS 2.0.4 –max-intronlen 300000 –novel-splicesite-
   infile {input.novel_splice}
   –novel-splicesite-outfile {output.novel_splice}
STAR v2.5.2b –twopassMode Basic –alignMatesGapMax
   300000
   –alignIntronMax 300000
STAR_fusion v2.5.2b –twopassMode Basic –alignMatesGapMax
   300000
   –alignIntronMax 300000 –chimSegmentMin
   –chimJunctionOverhangMin 12
   –chimSegmentReadGapMax 3
   12 –alignSJstitchMismatchNmax 5 -1 5 5
CRAC 2.5.0 -k 22 –detailed-sam –no-ambiguity –deep-snv
CRAC_fusion 2.5.0 -k 22 –detailed-sam –no-ambiguity –deep-
   snv –min-chimera-score 0
GATK 1.3.1 -T HaplotypeCaller -dontUseSoftClippedBases
   -stand_call_conf 20.0
   -stand_emit_conf 20.0
FREEBAYES 1.0.2 default
SAMTOOLS mpileup 1.3.1 default
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