This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds.
.TP
map_len
This takes effect in the “map” step and is the minimun alignment length between a read and a contig required for a reliable read location.
This takes effect in the “map” step and is the minimum alignment length between a read and a contig required for a reliable read location.
.P
The assembler accepts read file in two formats: FASTA or FASTQ.
Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair.
@@ -121,7 +121,7 @@ strength of merging similar sequences during contiging [default 1, min 0, max 3]
intra-scaffold gap closure [default no]
.TP
\-u
un-mask high coverage contigs before scaffolding [defaut mask]
un-mask high coverage contigs before scaffolding [default mask]
.IP "Information for each clone library: insert-size, read index upper bound, rank and pair number cutoff for a reliable link."
.IP "This file can be revised manually for scaffolding tuning."
.IP "b. *.readOnContig"
.IP "Read locations on contigs. Here contigs are referred by their edge index. Howerver about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."
.IP "Read locations on contigs. Here contigs are referred by their edge index. However about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."
.IP "c. *.readInGap"
.IP "This file includes reads that could be located in gaps between contigs. This information will be used to close gaps in scaffolds."
This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds.
.TP
map_len
This takes effect in the “map” step and is the minimun alignment length between a read and a contig required for a reliable read location.
This takes effect in the “map” step and is the minimum alignment length between a read and a contig required for a reliable read location.
.P
The assembler accepts read file in two formats: FASTA or FASTQ.
Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair.
@@ -121,7 +121,7 @@ strength of merging similar sequences during contiging [default 1, min 0, max 3]
intra-scaffold gap closure [default no]
.TP
\-u
un-mask high coverage contigs before scaffolding [defaut mask]
un-mask high coverage contigs before scaffolding [default mask]
.IP "Information for each clone library: insert-size, read index upper bound, rank and pair number cutoff for a reliable link."
.IP "This file can be revised manually for scaffolding tuning."
.IP "b. *.readOnContig"
.IP "Read locations on contigs. Here contigs are referred by their edge index. Howerver about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."
.IP "Read locations on contigs. Here contigs are referred by their edge index. However about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."
.IP "c. *.readInGap"
.IP "This file includes reads that could be located in gaps between contigs. This information will be used to close gaps in scaffolds."
This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds.
.TP
map_len
This takes effect in the “map” step and is the minimun alignment length between a read and a contig required for a reliable read location.
This takes effect in the “map” step and is the minimum alignment length between a read and a contig required for a reliable read location.
.P
The assembler accepts read file in two formats: FASTA or FASTQ.
Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair.
@@ -121,7 +121,7 @@ strength of merging similar sequences during contiging [default 1, min 0, max 3]
intra-scaffold gap closure [default no]
.TP
\-u
un-mask high coverage contigs before scaffolding [defaut mask]
un-mask high coverage contigs before scaffolding [default mask]
.IP "Information for each clone library: insert-size, read index upper bound, rank and pair number cutoff for a reliable link."
.IP "This file can be revised manually for scaffolding tuning."
.IP "b. *.readOnContig"
.IP "Read locations on contigs. Here contigs are referred by their edge index. Howerver about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."
.IP "Read locations on contigs. Here contigs are referred by their edge index. However about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."
.IP "c. *.readInGap"
.IP "This file includes reads that could be located in gaps between contigs. This information will be used to close gaps in scaffolds."
