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r213: renamed trio binning output files

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This commit is contained in:
Heng Li
2020-04-09 20:40:01 -04:00
parent c3f032da37
commit 7a35bd7fcc
5 changed files with 97 additions and 90 deletions
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hifiasm.1
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@@ -8,7 +8,7 @@ hifiasm - haplotype-resolved de novo assembler for PacBio Hifi reads.
.PP
hifiasm
.RB [ -o
.IR outPrefix ]
.IR prefix ]
.RB [ -t
.IR numThres ]
.RB [ -r
@@ -51,8 +51,8 @@ outputs consist of multiple types of assembly graph in GFA format.
.BI -o \ FILE
Prefix of output files [hifiasm.asm]. The outputs of hifiasm include error corrected
reads in fasta format, all-to-all overlaps in paf format, and four types of assembly
graph in GFA format. For detailed description of all assembly graphs, please see
.I 'Outputs'
graph in GFA format. For detailed description of all assembly graphs, please see the
.B OUTPUTS
section of this man-page.
.TP 10
@@ -83,11 +83,11 @@ Rounds of haplotype-aware error corrections [2]. This option affects all outputs
.TP 10
.BI -a \ INT
Rounds of assembly graph cleaning [4]. This option is used with
.I [-x maxDropRatio]
.B -x
and
.I [-y minDropRatio].
.BR -y .
Note that unlike
.I [-r],
.BR -r ,
this option does not affect error corrected reads and all-to-all overlaps.
@@ -103,11 +103,11 @@ significantly improve the assembly quality.
.TP 10
.BI -m \ INT
Maximal probing distance for bubble popping when generating primary/alternate assembly
Maximal probing distance for bubble popping when generating primary/alternate
contig graphs [10000000]. Bubbles longer than
.I INT
bases will not be popped. For detailed description of these graphs, please see
.I 'Outputs'
bases will not be popped. For detailed description of these graphs, please see the
.B OUTPUTS
section of this man-page.
@@ -117,8 +117,8 @@ Maximal probing distance for bubble popping when generating haplotype-resolved p
without small bubbles [100000]. Bubbles longer than
.I INT
bases will not be popped. Small bubbles might be caused by somatic mutations or noise in data, which
are not the real haplotype information. For detailed description of this graph, please see
.I 'Outputs'
are not the real haplotype information. For detailed description of this graph, please see the
.B OUTPUTS
section of this man-page.
@@ -133,7 +133,7 @@ reads [3]. Hifiasm may try to remove small unitigs at various steps.
.TP 10
.BI -x \ FLOAT, -y \ FLOAT
Max and min overlap drop ratio [0.8, 0.2]. This option is used with
.I [-r roundCorrection].
.BR -r .
Given a node
.I N
in the assembly graph, let max(N)
@@ -143,15 +143,15 @@ Hifiasm iteratively drops overlaps of
.I N
if their length / max(N)
are below a threshold controlled by
.I [-x maxDropRatio]
.B -x
and
.I [-y minDropRatio].
.BR -y .
Hifiasm applies
.I [-r roundCorrection]
.B -r
rounds of short overlap removal with an increasing threshold between
.I [-x maxDropRatio]
.B -x
and
.I [-y minDropRatio].
.BR -y .
.TP 10
.BI -i
@@ -167,38 +167,37 @@ with different parameters.
.SS Trio-partition options
.TP 10
.BI -P \ FILE
Paternal trio index. This index should be generated by
.I [yak count]
with the paternal short reads. For details of yak, please see
.BI -1 \ FILE
Paternal/haplotype1 k-mer dump generated by
.B yak count
from the paternal/haplotype1 reads. For details of yak, please see
.I [https://github.com/lh3/yak]
.TP 10
.BI -M \ FILE
Maternal trio index. This index should be generated by
.I [yak count]
with the maternal short reads. For details of yak, please see
.BI -2 \ FILE
Maternal/haplotype2 k-mer dump generated by
.B yak count
from the maternal/haplotype2 reads. For details of yak, please see
.I [https://github.com/lh3/yak]
.TP 10
.BI -c \ INT
Lower bound of the binned k-mer's frequency [2]. When doing trio binning,
a k-mer is said to be differentiating if it occurs >=
.I [-d upper_bound]
.B -d
times in one sample
but occurs <
.I [-c lower_bound]
.B -c
times in the other sample.
.TP 10
.BI -d \ INT
Upper bound of the binned k-mer's frequency [5]. When doing trio binning,
a k-mer is said to be differentiating if it occurs >=
.I [-d upper_bound]
.B -d
times in one sample
but occurs <
.I [-c lower_bound]
.B -c
times in the other sample.
@@ -235,60 +234,69 @@ Build maternal trio index from mat.fq.gz.
Build paternal trio index from pat.fq.gz.
.TP
.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-P " " pat.yak " " \-M " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
In this example, hifiasm will do trio assembly with 32 CPU threads. The paternal assembly can be found at [NA12878.asm.p.r_utg.gfa],
and the maternal assembly can be found at [NA12878.asm.m.r_utg.gfa].
.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-1 " " pat.yak " " \-2 " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
In this example, hifiasm will do trio assembly with 32 CPU threads. The paternal assembly can be found at [NA12878.asm.hap1.p_ctg.gfa],
and the maternal assembly can be found at [NA12878.asm.hap2.p_ctg.gfa].
.SH OUTPUTS
.PP
Without trio partition options
.B -1
and
.BR -2 ,
hifiasm generates the following assembly graphs in the GFA format:
.RS 2
.TP 2
*
.IR prefix .r_utg.gfa:
haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
.TP
*
.IR prefix .p_utg.gfa:
haplotype-resolved processed unitig graph without small bubbles. Small bubbles
might be caused by somatic mutations or noise in data, which are not the real
haplotype information. The size of popped small bubbles should be specified by
.BR -p .
.TP
*
.IR prefix .p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
.TP
*
.IR prefix .a_ctg.gfa:
assembly graph of alternate contigs. This graph consists of all assemblies that
are discarded in primary contig graph.
.RE
.PP
Consider the prefix of output files has been specified by
.I [-o outPrefix].
During the error correction step, hifiasm outputs the following two files:
With trio partition, hifiasm outputs the following assembly graphs:
.IP
1. Haplotype-aware error corrected reads in fasta format [outPrefix.ec.fa].
.RS 2
.TP 2
*
.IR prefix .dip.r_utg.gfa:
haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
2. All-to-all overlaps in paf format [outPrefix.ovlp.paf].
.PP
During the non-trio assembly step, hifiasm outputs the following four assembly graphs in GFA format:
.IP
1. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
This graph keeps all haplotype information.
2. Haplotype-resolved processed unitig graph without small bubbles [outPrefix.p_utg.gfa].
Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.
The size of popped small bubbles should be specified by
.I [-p maxSmallBubbles].
3. Primary assembly contig graph [outPrefix.p_ctg.gfa].
This graph collapses different haplotypes.
4. Alternate assembly contig graph [outPrefix.a_ctg.gfa].
This graph consists of all assemblies that are discarded in primary assembly contig graph.
.PP
If you have trio information, hifiasm outputs the following three assembly graphs in GFA format:
.IP
1. Phased maternal unitig graph [outPrefix.m.r_utg.gfa].
This graph keeps the phased maternal assembly.
2. Phased paternal unitig graph [outPrefix.p.r_utg.gfa].
This graph keeps the phased paternal assembly.
3. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
This graph keeps all haplotype information.
.TP
*
.IR prefix .hap1.p_ctg.gfa:
phased paternal/haplotype1 contig graph. This graph keeps the phased
paternal/haplotype1 assembly.
.TP
*
.IR prefix .hap2.p_ctg.gfa:
phased maternal/haplotype2 contig graph. This graph keeps the phased
maternal/haplotype2 assembly.
.RE
.PP
For each graph, hifiasm also outputs a simplified version without sequences. These simplified