BWA_XSEDE

Input files:
Dbin_ = reference database sequences in fasta format
Queryin_ = query1.fq.gz
queryinpair_ = query2.fq.gz

Parmeters:
runtime_ = float. Default=0.25
BWA index options
Pvalue_= Switch, Submitting a single interleaved fastq? default=0
indexalg_ = Excl, Indexing algorithm, allowed:is or bwstw, default=is                             <           
colorspace_ = Switch, Build color-space index? (default=0)
SAM_NAME_ = String, Output File Name , default = aln.sam
 
Options for bwa mem
Pvalue2_ = Switch, Submitting a single interleaved fastq? (default -0)
 
Other available options
<!-- bwa mem -M -t 16 TSWV_genome.fasta 1_S1_L001.1.paired.fq.gz 1_S1_L001.2.paired.fq.gz > 1_S1_L001.1_mem.sam
Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]
 
Algorithm options:
 
       -t INT        number of threads [16]
       -k INT        minimum seed length [19]
       -w INT        band width for banded alignment [100]
       -d INT        off-diagonal X-dropoff [100]
       -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
       -y INT        seed occurrence for the 3rd round seeding [20]
       -c INT        skip seeds with more than INT occurrences [500]
       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]
       -W INT        discard a chain if seeded bases shorter than INT [0]
       -m INT        perform at most INT rounds of mate rescues for each read [50]
       -S            skip mate rescue
       -P            skip pairing; mate rescue performed unless -S also in use
 
Scoring options:
 
       -A INT        score for a sequence match, which scales options -TdBOELU unless overridden [1]
       -B INT        penalty for a mismatch [4]
       -O INT[,INT]  gap open penalties for deletions and insertions [6,6]
       -E INT[,INT]  gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]
       -L INT[,INT]  penalty for 5'- and 3'-end clipping [5,5]
       -U INT        penalty for an unpaired read pair [17]
 
       -x STR        read type. Setting -x changes multiple parameters unlessoverriden [null]
                     pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  (PacBio reads to ref)
                     ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0  (OxfordNanopore 2D-reads to ref)
                     intractg: -B9 -O16 -L5  (intra-species contigs to ref)
 
Input/output options:
 
       -p            smart pairing (ignoring in2.fq)
       -R STR        read group header line such as '@RG\tID:foo\tSM:bar' [null]
       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]
       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)
 
       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]
       -T INT        minimum score to output [30]
       -h INT[,INT]  if there are <INT hits with score >80% of the max score, output all in XA [5,200]
       -a            output all alignments for SE or unpaired PE
       -C            append FASTA/FASTQ comment to SAM output
       -V            output the reference FASTA header in the XR tag
       -Y            use soft clipping for supplementary alignments
       -M            mark shorter split hits as secondary
 
       -I FLOAT[,FLOAT[,INT[,INT]]]
                     specify the mean, standard deviation (10% of the mean if absent), max
                     (4 sigma from the mean if absent) and min of the insert size distribution.
                     FR orientation only. [inferred]