table of contents
| REAPR-SMALTMAP(1) | REAPR-SMALTMAP(1) |
NAME¶
reapr-smaltmap - map read pairs using SMALT
SYNOPSIS¶
reapr smaltmap [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq> <out.bam>
DESCRIPTION¶
Maps read pairs to an assembly with SMALT, making a final BAM file that is sorted, indexed and has duplicates removed.
The n-th read in <reads_1.fastq> should be the mate of the n-th read in <reads_2.fastq>.
It is assumed that reads are 'innies', i.e. the correct orientation is reads in a pair pointing towards each other (--→ ←--).
OPTIONS¶
-k <int>
The -k option (kmer hash length) when indexing the genome
with 'smalt index' [13]
-s <int>
The -s option (step length) when indexing the genome with
'smalt index' [2]
-m <int>
The -m option when mapping reads with 'smalt map' [not
used by default]
-n <int>
The number of threads used when running 'smalt map'
[1]
-y <float>
The -y option when mapping reads with 'smalt map'. The default of 0.5 means that at least 50% of each read must map perfectly. Depending on the quality of your reads, you may want to increase this to be more stringent (or consider using -m) [0.5]
-x
Use this to just print the commands that will be run, instead of actually running them
-u <int>
The -u option of 'smalt sample'. This is used to estimate the insert size from a sample of the reads, by mapping every n^th read pair [1000]