Short read aligner comparison

From CSBLwiki

BFAST

http://dna.cs.byu.edu/gnumap/

http://iga-rna.sourceforge.net/

http://samtools.sourceforge.net/swlist.shtml

http://bamview.sourceforge.net/

SAM protocol

This is explained in the manual page. Or briefly (when you invoke pileup with the -c option):

1. reference sequence name
2. reference coordinate
3. reference base, or `*' for an indel line
4. genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, */+A, -A/* or +CC/-C. There is no difference between */+A or +A/*.
5. Phred-scaled likelihood that the genotype is wrong, which is also called `consensus quality'.
6. Phred-scaled likelihood that the genotype is identical to the reference, which is also called `SNP quality'. Suppose the reference base is A and in alignment we see 17 G and 3 A. We will get a low consensus quality because it is difficult to distinguish an A/G heterozygote from a G/G homozygote. We will get a high SNP quality, though, because the evidence of a SNP is very strong.
7. root mean square (RMS) mapping quality
8. # reads covering the position
9. read bases at a SNP line (check the manual page for more information); the 1st indel allele otherwise
10. base quality at a SNP line; the 2nd indel allele otherwise
11. indel line only: # reads directly supporting the 1st indel allele
12. indel line only: # reads directly supporting the 2nd indel allele
13. indel line only: # reads supporting a third indel allele

If pileup is invoked without `-c', indel lines and columns between 3 and 7 inclusive will not be outputted.

$ fastq_quality_filter -h

	usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE]

	version 0.0.6
	   [-h]         = This helpful help screen.
	   [-q N]       = Minimum quality score to keep. 
	   [-p N]       = Minimum percent of bases that must have [-q] quality.
	   [-z]         = Compress output with GZIP.
	   [-i INFILE]  = FASTA/Q input file. default is STDIN.
	   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
	   [-v]         = Verbose - report number of sequences.
			  If [-o] is specified,  report will be printed to STDOUT.
			  If [-o] is not specified (and output goes to STDOUT),
			  report will be printed to STDERR.