From f83ee141fe732603475cb22c56995cec491354eb Mon Sep 17 00:00:00 2001 From: martin Date: Mon, 26 Sep 2016 11:19:25 +0200 Subject: [PATCH] fix small typos in README.md --- README.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 38c69c0..253b47a 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. -## Requirement +## Requirements This software is suitable for all unix-like system with gcc installed. @@ -25,7 +25,7 @@ This software is suitable for all unix-like system with gcc installed. $ ./build.sh ### If you use the release package. -Exract the package, then use make to compile the source code. +Extract the package, then use make to compile the source code. ``` $ ./configure $ make @@ -37,7 +37,7 @@ $ make IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a -generic purpose assembler and epspacially good for single-cell and metagenomic sequencing data. +generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data. @@ -59,29 +59,29 @@ Please find the manual by running the assembler without any parameters. For exam $ bin/idba ``` -IDBA series assemblers accept fasta format reads. Fastq format reads can be converted by -fq2fa program in the packcage. +IDBA series assemblers accept FASTA format reads. FASTQ format reads can be converted by +fq2fa program in the package. ``` $ bin/fq2fa read.fq read.fa ``` -IDBA-UD IDBA-Hybrid and IDBA-Tran require paired-end reads stored in single FastA file and a pair of -reads is in consecutive two lines. If not, please use fq2fa to merge two -FastQ read files to single file. +IDBA-UD, IDBA-Hybrid and IDBA-Tran require paired-end reads stored in the same FASTA file. A pair of +reads should be in two consecutive lines. If not, please use fq2fa to merge two +FASTQ read files to single file. ``` $ bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa ``` -or convert a FastQ read file to FastA file. +or convert a FASTQ read file to FASTA file. ``` $ bin/fq2fa --paired --filter read.fq read.fa ``` -The this tools assume the paired-end reads are in order (->, <-). If your data is in order (<-, ->), +This tool assumes that the paired-end reads are in order (->, <-). If your data is in reverse order (<-, ->), please convert it by yourself. ## IDBA on Docker -A docker image was built for IDBA. Please use the follow command to run IDBA-UD on Docker (Assuming -the input read file is in current directory). **If you are using Mac os and see bus error, please try +A docker image was built for IDBA. Please use the following command to run IDBA-UD on Docker (assuming +the input read file is in the current directory). **If you are using Mac OS and see bus error, please try this image.** ``` $ docker run -v `pwd`:/data -w /data loneknightpy/idba idba_ud -r read.fa -o output