From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: typo fixes, courtesy lintian
--- abyss.orig/Sealer/README.md
+++ abyss/Sealer/README.md
@@ -24,7 +24,7 @@
 Description
 ===========
 
-Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, succesfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.
+Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, successfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.
 
 Installation
 ============
@@ -159,6 +159,6 @@
 * `--help`: display this help and exit
 * `--version`: output version information and exit
 
-*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the nubmer of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.
+*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the number of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.
 
 *P* is the threshold for number of paths allowed to be traversed. When set to 10, Konnector will attempt to close gaps even when there are 10 different paths found. It would attempt to create a consensus sequence between these paths. The default setting is 2.
--- abyss.orig/doc/abyss-pe.1
+++ abyss/doc/abyss-pe.1
@@ -113,7 +113,7 @@
 SS=--SS to assemble in strand-specific mode
 .br
 Requires that all libraries are strand-specific RNA-Seq libraries.
-Assumes that the first read in a read pair is reveresed WRT the
+Assumes that the first read in a read pair is reversed WRT the
 transcripts sequenced.
 .TP
 .B t
@@ -242,7 +242,7 @@
 
 .SS "MPI COMPATIBILITY"
 Due to its use of multi-threading, DIDA has known deadlocking issues
-with OpenMPI.  Using the MPICH MPI library is strongly recommmended
+with OpenMPI.  Using the MPICH MPI library is strongly recommended
 when running assemblies with DIDA. Testing was done with MPICH 3.1.3,
 compiled with --enable-threads=funneled.
 
