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 |