表观遗传学——数据的回贴与比对

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Bowtie与Bowtie2的比较

Bowtie不支持gap，Bowtie2支持gap

HISAT2支持DNA比对
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

bwa
Fast and accurate short read alignment with Burrows-Wheeler transform
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

• Bowtie主要应用于无gap的短序列比对
• Bowtie2主要应用于无大结构变异的比对
  • Chip-seq，Hi-C
• BWA MEM算法非常适合全基因组，外显子组测序

bowtie

• Alignment:
  • -v report end-to-end hits w/ <=v mismatches; ignore qualities
    or
  • -n/--seedmms max mismatches in seed (can be 0-3, default: -n 2)
  • -e/--maqerr max sum of mismatch quals across alignment for -n (def: 70)
  • -l/--seedlen seed length for -n (default: 28)
  • --nomaqround disable Maq-like quality rounding for -n (nearest 10 <= 30)
  • -I/--minins minimum insert size for paired-end alignment (default: 0)
  • -X/--maxins maximum insert size for paired-end alignment (default: 250)
  • --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)
  • --nofw/--norc do not align to forward/reverse-complement reference strand
  • --maxbts max # backtracks for -n 2/3 (default: 125, 800 for --best)
  • --pairtries max # attempts to find mate for anchor hit (default: 100)
  • -y/--tryhard try hard to find valid alignments, at the expense of speed--chunkmbs max megabytes of RAM for best-first search frames (def: 64)
  • --reads-per-batch # of reads to read from input file at once (default: 16)
• Reporting:
  • -k report up to good alignments per read (default: 1)
  • -a/--all report all alignments per read (much slower than low -k)
  • -m suppress all alignments if > exist (def: no limit)
  • -M like -m, but reports 1 random hit (MAPQ=0); requires --best
  • --best hits guaranteed best stratum; ties broken by quality
  • --strata hits in sub-optimal strata aren't reported (requires --best)

bowtie2

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• Alignment:
  • -N max # mismatches in seed alignment; can be 0 or 1 (0)
  • -L length of seed substrings; must be >3, <32 (22)
  • -i interval between seed substrings w/r/t read len (S,1,1.15)
  • --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  • --dpad include extra ref chars on sides of DP table (15)
  • --gbar disallow gaps within nucs of read extremes (4)
  • --ignore-quals treat all quality values as 30 on Phred scale (off)
  • --nofw do not align forward (original) version of read (off)
  • --norc do not align reverse-complement version of read (off)
  • --no-1mm-upfront do not allow 1 mismatch alignments before attempting to scan for the optimal seeded alignments
  • --end-to-end entire read must align; no clipping (on) OR
  • --local local alignment; ends might be soft clipped (off)

bowtie-build ref1.fa ref1.fa
bowtie2-build ref1.fa ref1.fa
bwa index ref1.fa ref1.fa