Usage: biscuit align [options] <fai-index base> <in1.fq> [in2.fq]
Algorithm options:
-@ INT Number of threads [1]
-b INT For PE, map read 1 to parent, read 2 to daughter
(1: directional library) or read1 and read 2 to both
(0: non-directional library [default]). For SE, parent
(1), daughter (3), or both (0 [default]). Note, parent
is the bisulfite treated strand and the daughter is
the complement strand.
-f INT 1: BSW strand; 3: BSC strand; 0: both. Note, libraries
targeting either BSW or BSC are unseen so far! [0]
-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 of seeding [20]
-J STR Adaptor of read 1 (fastq direction)
-K STR Adaptor of read 2 (fastq direction)
-z INT Minimum base quality to keep from both ends of reads [0]
-5 INT Number of extra bases to clip from 5'-end [0]
-3 INT Number of extra bases to clip from 3'-end [0]
-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 a read [50]
-S Skip mate rescue
-P Skip pairing - mate rescue performed unless -S also given
-e Discard full-length exact matches
-9 Extract barcode from read comment
Scoring options:
-A INT Score for a sequence match, scales options -TdBOELU unless
overridden [1]
-B INT Penalty for a mismatch [2]
-O INT[,INT] Gap open penalties for deletions and insertions [6,6]
-E INT[,INT] Gap extension penalty; a gap of size, g, has penalty
{-O} + {-E}*g [1,1]
-L INT[,INT] Penalty for 5'- and 3'-end clipping [10,10]
-U INT Penalty for an unpaired read pair [17]
Input/output options:
-1 STR Align a single read STR
-2 STR Align a read STR paired with -1 read
-i Turn off autoinference of ALT chromosomes
-p Smart pairing (ignores in2.fq)
-R STR Read group header line (such as '@RG\tID:foo\tSM:bar')
-F Suppress SAM header output
-H STR/FILE Insert STR to header if it starts with @ or insert lines
in FILE
-j Treat ALT contigs as part of the primary assembly (i.e.
ignore <fai-index base>.alt file)
-q Do not modify mapQ of supplementary alignments
-T INT Minimum score to output [30]
-g INT[,INT] Maximum number of hits output in XA [5,5]
-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), maximum (4 sigma from the mean if absent)
and minimum of insert size distribution. FR orientation
only [inferred]
-v INT Verbosity level:
1: error, 2: warning, 3: message, 4+: debugging [3]
-h This help